From 008bf69d684e822d21294b6508fef615b58339eb Mon Sep 17 00:00:00 2001 From: Javier Herrero Date: Mon, 6 Jul 2015 11:24:10 +0100 Subject: [PATCH 01/26] Update title for new v1.1 version --- webserver/cgi-bin/index.pl | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/webserver/cgi-bin/index.pl b/webserver/cgi-bin/index.pl index dedcfa7..ba50234 100755 --- a/webserver/cgi-bin/index.pl +++ b/webserver/cgi-bin/index.pl @@ -47,7 +47,7 @@ my $colour="bright-blue"; my $plot_colour="#29A6C9"; -my $title = "eFORGE"; +my $title = "eFORGE v1.1"; my $breadcrumbs = [ {"UCL Cancer Institute" => "http://www.ucl.ac.uk/cancer"}, @@ -57,7 +57,7 @@ my $left_menu = [ {"__logo__" => "$WEB_ROOT/img/logo.jpg"}, - {"__title__" => "eFORGE"}, + {"__title__" => $title}, {"Start" => "$WEB_ROOT/"}, {"Help" => "$WEB_ROOT/?help"}, {"Documentation" => "$WEB_ROOT/?documentation"}, @@ -494,7 +494,7 @@ sub run_tool { my $web_outdir = get_web_outdir(); my $url = $q->url(-base=>1)."$web_outdir/index.html"; my @output = qx"cat $absolute_outdir/$STDOUT_FILE"; - print INDEX Template::header("eFORGE"); + print INDEX Template::header($title); print INDEX Template::content_box("Done.", "".join(" ", "perl", "eforge.pl", "-f", "input.txt", @$validated_args). "", @@ -638,7 +638,7 @@ sub print_waiting_page { my $start = Template::start($title, $breadcrumbs, $left_menu, $colour, $right_column); $start =~ s/(\s+)/<noscript><META HTTP-EQUIV="refresh" CONTENT="$REFRESH_TIME;URL=$url" id="reload"><\/noscript>$1/i; print $fh $start; - print $fh Template::header("eFORGE"); + print $fh Template::header($title); print $fh Template::content_box("<div id=\"status_title\">Running...</div>", "<strong>".join(" ", "perl", "eforge.pl", "-f", "input.txt", @$validated_args). "</strong>", @@ -825,7 +825,7 @@ =head2 print_help_page sub print_help_page { print $q->header; print Template::start($title, $breadcrumbs, $left_menu, $colour, $right_column); - print Template::header("eFORGE > Help"); + print Template::header("$title > Help"); print_intro_box(); @@ -937,7 +937,7 @@ =head2 print_documentation_page sub print_documentation_page { print $q->header; print Template::start($title, $breadcrumbs, $left_menu, $colour, $right_column); - print Template::header("eFORGE > Documentation"); + print Template::header("$title > Documentation"); print Template::content_box("eFORGE analysis tool", "The eFORGE (<u>e</u>xperimentally-derived <u>F</u>unctional element <u>O</u>verlap analysis of <u>R</u>e<u>G</u>ions from <u>E</u>WAS) tool performs a Functional Overlap analysis to identify tissue specific signal for a given set of EWAS DMPs.<br \>", @@ -993,7 +993,7 @@ =head2 print_download_page sub print_download_page { print $q->header; print Template::start($title, $breadcrumbs, $left_menu, $colour, $right_column); - print Template::header("eFORGE > Download"); + print Template::header("$title > Download"); print Template::content_box("Download", "The code is available on GitHub: <a href=\"https://github.com/charlesbreeze/eFORGE\">https://github.com/charlesbreeze/eFORGE</a>", @@ -1042,7 +1042,7 @@ =head2 print_about_page sub print_about_page { print $q->header; print Template::start($title, $breadcrumbs, $left_menu, $colour, $right_column); - print Template::header("eFORGE > About"); + print Template::header("$title > About"); print Template::content_box("eFORGE", "eFORGE was developed by <a href=\"http://www.ucl.ac.uk/cancer/medical-genomics/mg_staff\">Charles Breeze</a> while on secondment at the From a61d7ee452d094cce11ff42b33536c4d92c26e49 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Tue, 29 Sep 2015 08:55:18 +0100 Subject: [PATCH 02/26] Use a refarray instead of an array for mvps --- eforge.pl | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/eforge.pl b/eforge.pl index b0d8ac3..d0faef3 100644 --- a/eforge.pl +++ b/eforge.pl @@ -294,7 +294,7 @@ =head1 CONTACT my $dbh = DBI->connect($dsn, "", "") or die $DBI::errstr; # mvps need to come either from a file or a list -my @mvps; +my $mvps; # A series of data file formats to accept. @@ -309,23 +309,23 @@ =head1 CONTACT } my $sth = $dbh->prepare("SELECT probeid FROM bits WHERE location = ?"); open my $fh, "<", $file or die "cannot open file $file : $!"; - @mvps = process_file($fh, $format, $sth, $filter); + @$mvps = process_file($fh, $format, $sth, $filter); } elsif (@mvplist) { - @mvps = split(/,/,join(',',@mvplist)); + @$mvps = split(/,/,join(',',@mvplist)); } else{ # Test MVPs from Liu Y et al. Nat Biotechnol 2013 Pulmonary_function.snps.bed (*put EWAS bedfile here) # If no options are given it will run on the default set of MVPs warn "No probe input given, so running on default set of probes, a set of monocyte tDMPs from Jaffe AE and Irizarry RA, Genome Biol 2014."; - @mvps = qw(cg13430807 cg10480329 cg06297318 cg19301114 cg23244761 cg26872907 cg18066690 cg04468741 cg16636767 cg10624395 cg20918393); + @$mvps = qw(cg13430807 cg10480329 cg06297318 cg19301114 cg23244761 cg26872907 cg18066690 cg04468741 cg16636767 cg10624395 cg20918393); } # Remove redundancy in the input my %nonredundant; -foreach my $mvp (@mvps) { +foreach my $mvp (@$mvps) { $nonredundant{$mvp}++; } @@ -336,25 +336,25 @@ =head1 CONTACT } } -@mvps = keys %nonredundant; -my @origmvps = @mvps; +@$mvps = keys %nonredundant; +my @origmvps = @$mvps; #######!!!!!### proximity filtering starts below: my ($prox_excluded, $output, $input); unless(defined $noproxy) { - $input = scalar @mvps; - ($prox_excluded, @mvps) = prox_filter(\@mvps, $dbh); + $input = scalar @$mvps; + ($prox_excluded, @$mvps) = prox_filter($mvps, $dbh); while (my ($excluded_mvp, $mvp) = each %$prox_excluded) { warn "$excluded_mvp excluded for proximity (1 kb) with $mvp\n"; } - $output = scalar @mvps; + $output = scalar @$mvps; } # Check we have enough MVPs -if (scalar @mvps < $min_mvps) { +if (scalar @$mvps < $min_mvps) { die "Fewer than $min_mvps MVPs. Analysis not run\n"; } @@ -363,7 +363,7 @@ =head1 CONTACT my ($cells, $tissues) = get_cells($data, $dbh); # get the bit strings for the test mvps from the database file -my $rows = get_bits(\@mvps, $dbh); +my $rows = get_bits($mvps, $dbh); # unpack the bitstrings and store the overlaps by cell. my $test = process_bits($rows, $cells, $data); @@ -395,7 +395,7 @@ =head1 CONTACT } if (defined $proxy) { if ($output < $input) { - warn "For $label, $input MVPs provided, " . scalar @mvps . " retained, " . scalar @missing . " not analysed, " . scalar(keys %$prox_excluded) . " proximity filtered at 1 kb\n"; + warn "For $label, $input MVPs provided, " . scalar @$mvps . " retained, " . scalar @missing . " not analysed, " . scalar(keys %$prox_excluded) . " proximity filtered at 1 kb\n"; } } From 48e0d8b71948be0b7754d3c709a8be1669f2a2ce Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Tue, 29 Sep 2015 09:30:36 +0100 Subject: [PATCH 03/26] Fix legacy from FORGE in process_file and fetch_rsid (now called fetch_probe_id) --- eForge/eForge.pm | 121 +++++++++++++++++++++---------------------------------- eforge.pl | 2 +- 2 files changed, 47 insertions(+), 76 deletions(-) diff --git a/eForge/eForge.pm b/eForge/eForge.pm index 824262d..dd077f2 100644 --- a/eForge/eForge.pm +++ b/eForge/eForge.pm @@ -75,77 +75,49 @@ Processes various file formats. sub process_file { my ($fh, $format, $sth, $filter) = @_; - my @snps; - if ($format =~ /probeid/){ - while (<$fh>){ + my $probe_ids = []; + + if ($format =~ /^probe/i) { + while (<$fh>) { next if /^#/; chomp; - my $rs; + my $probe_id; if (defined $filter) { my $pval; - ($rs, $pval) = split /\s+/, $_; + ($probe_id, $pval) = split /\s+/, $_; next unless $pval >= $filter; - } - else{ - ($rs, undef) = split /\s+/, $_; # remove anything that is not supposed to be there :-) - } - my @rsid = split /\:/, $rs; - my $rsid = pop @rsid; # take the last one for want of a better idea. - push @snps, $rsid; - } - } - elsif ($format =~ /ian/){ - while (<$fh>){ - my ($chr, $beg, $end, $rsid, $p, $pval) = split "\t", $_; - if (defined $filter) { - next unless $pval >= $filter; - } - my @rsid = split /\:/, $rsid; # to deal with multiple rsids - $rsid = pop @rsid; # take the last one for want of a better idea. Can't take all as they are the same thing. - push @snps, $rsid; - } - } - elsif ($format =~ /vcf/){ - while (<$fh>){ - next if /^#/; - my ($chr, $beg, $rsid) = split "\t", $_; + } else { + ($probe_id, undef) = split /\s+/, $_; # remove anything that is not supposed to be there :-) + } + push @$probe_ids, $probe_id; + } + + } elsif ($format =~ /^bed/i) { + while (<$fh>) { + next if /^track/; + chomp; + my ($chr, $beg, $end) = split "\t", $_; + next if (!defined($end)); unless ($chr =~ /^chr/){ $chr = "chr". $chr; - } - if ($rsid =~ /^cg\d+/){ - push @snps, $rsid; - } - else { - my $loc = "$chr:$beg-$beg"; - #get the rsid from the db - $rsid = fetch_rsid($loc, $sth); - push @snps, $rsid if defined $rsid; - } - } - } - elsif ($format =~ /bed|tabix/){ - while (<$fh>){ - my $loc; - if ($format =~/bed/){ - next if /^track/; - chomp; - my ($chr, $beg, $end) = split "\t", $_; - unless ($chr =~ /^chr/){ - $chr = "chr". $chr; - } - $loc = "$chr:$beg-$beg"; - } - elsif ($format =~ /tabix/){ - chomp; - $loc = $_; - } - #get the $rsid from the db - my $rsid = fetch_rsid($loc, $sth); - push @snps, $rsid if defined $rsid; - } - } - return @snps; - } + } + my $loc = "$chr:$beg-$beg"; + #get the $probe_id from the db + my $probe_id = fetch_probe_id($loc, $sth); + push @$probe_ids, $probe_id if defined $probe_id; + } + + } elsif ($format =~ /^tabix/i) { + while (<$fh>) { + chomp; + my $loc = $_; + #get the $probe_id from the db + my $probe_id = fetch_probe_id($loc, $sth); + push @$probe_ids, $probe_id if defined $probe_id; + } + } + return $probe_ids; +} =head2 match @@ -320,23 +292,22 @@ gets the rsid for a SNP where a location is given. =cut -sub fetch_rsid{ +sub fetch_probe_id { #gets the rsid for a SNP where a location is given my ($loc, $sth) = @_; $sth->execute($loc); my $result = $sth->fetchall_arrayref(); - my $rsid; - foreach my $row (@{$result}){ - $rsid = $$row[0]; - } + my $probe_id; + foreach my $row (@{$result}) { + $probe_id = $$row[0]; + } $sth->finish(); - if (defined $rsid &&$rsid =~ /^cg\d+/){ - return $rsid; - } - else{ + if (defined $probe_id &&$rsid =~ /^cg\d+/) { + return $probe_id; + } else { return "no PROBEID match for $loc"; - } - } + } +} =head2 prox_filter diff --git a/eforge.pl b/eforge.pl index d0faef3..539915c 100644 --- a/eforge.pl +++ b/eforge.pl @@ -309,7 +309,7 @@ =head1 CONTACT } my $sth = $dbh->prepare("SELECT probeid FROM bits WHERE location = ?"); open my $fh, "<", $file or die "cannot open file $file : $!"; - @$mvps = process_file($fh, $format, $sth, $filter); + $mvps = process_file($fh, $format, $sth, $filter); } elsif (@mvplist) { @$mvps = split(/,/,join(',',@mvplist)); From ed1b556fb74260865094303b6581b7aa0eb61a22 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Tue, 29 Sep 2015 09:39:55 +0100 Subject: [PATCH 04/26] Fix bug about remaining variable --- eForge/eForge.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/eForge/eForge.pm b/eForge/eForge.pm index dd077f2..612fd45 100644 --- a/eForge/eForge.pm +++ b/eForge/eForge.pm @@ -302,7 +302,7 @@ sub fetch_probe_id { $probe_id = $$row[0]; } $sth->finish(); - if (defined $probe_id &&$rsid =~ /^cg\d+/) { + if (defined $probe_id && $probe_id =~ /^cg\d+/) { return $probe_id; } else { return "no PROBEID match for $loc"; From 10a29b31086bd1aef1ca05b51e878f0b53044739 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Tue, 29 Sep 2015 09:41:43 +0100 Subject: [PATCH 05/26] Move SQL for fetching probe_id from location to eForge.pm --- eForge/eForge.pm | 11 +++++++---- eforge.pl | 3 +-- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/eForge/eForge.pm b/eForge/eForge.pm index 612fd45..59d15a4 100644 --- a/eForge/eForge.pm +++ b/eForge/eForge.pm @@ -74,7 +74,7 @@ Processes various file formats. =cut sub process_file { - my ($fh, $format, $sth, $filter) = @_; + my ($fh, $format, $dbh, $filter) = @_; my $probe_ids = []; if ($format =~ /^probe/i) { @@ -103,7 +103,7 @@ sub process_file { } my $loc = "$chr:$beg-$beg"; #get the $probe_id from the db - my $probe_id = fetch_probe_id($loc, $sth); + my $probe_id = fetch_probe_id($dbh, $loc); push @$probe_ids, $probe_id if defined $probe_id; } @@ -112,7 +112,7 @@ sub process_file { chomp; my $loc = $_; #get the $probe_id from the db - my $probe_id = fetch_probe_id($loc, $sth); + my $probe_id = fetch_probe_id($dbh, $loc); push @$probe_ids, $probe_id if defined $probe_id; } } @@ -294,7 +294,10 @@ gets the rsid for a SNP where a location is given. sub fetch_probe_id { #gets the rsid for a SNP where a location is given - my ($loc, $sth) = @_; + my ($dbh, $loc) = @_; + + my $sth = $dbh->prepare_cached("SELECT probeid FROM bits WHERE location = ?"); + $sth->execute($loc); my $result = $sth->fetchall_arrayref(); my $probe_id; diff --git a/eforge.pl b/eforge.pl index 539915c..a09c517 100644 --- a/eforge.pl +++ b/eforge.pl @@ -307,9 +307,8 @@ =head1 CONTACT warn "You have specified p value filtering, but this isn't implemented for files of format $format. No filtering will happen." } } - my $sth = $dbh->prepare("SELECT probeid FROM bits WHERE location = ?"); open my $fh, "<", $file or die "cannot open file $file : $!"; - $mvps = process_file($fh, $format, $sth, $filter); + $mvps = process_file($fh, $format, $dbh, $filter); } elsif (@mvplist) { @$mvps = split(/,/,join(',',@mvplist)); From 43d71125f731eb3a0e180074ef4af8f9ce2b9bf7 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Wed, 30 Sep 2015 06:58:03 +0100 Subject: [PATCH 06/26] Copyright and authorship --- AUTHORS | 3 + COPYING | 621 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ eForge/eForge.pm | 61 +++--- eForge/ePlot.pm | 71 +++---- eForge/eStats.pm | 77 +++---- eforge.pl | 29 +-- 6 files changed, 717 insertions(+), 145 deletions(-) create mode 100644 AUTHORS create mode 100644 COPYING diff --git a/AUTHORS b/AUTHORS new file mode 100644 index 0000000..16a081a --- /dev/null +++ b/AUTHORS @@ -0,0 +1,3 @@ +eFORGE was initially developed by Charles Breeze while on secondment at the European Bioinformatics Institute as part of the EpiTrain Initial Training Network. + +The code, webserver and database are currently maintained by Charles Breeze and Javier Herrero. diff --git a/COPYING b/COPYING new file mode 100644 index 0000000..94a0453 --- /dev/null +++ b/COPYING @@ -0,0 +1,621 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS diff --git a/eForge/eForge.pm b/eForge/eForge.pm index 59d15a4..34e729f 100644 --- a/eForge/eForge.pm +++ b/eForge/eForge.pm @@ -7,12 +7,36 @@ use Storable; =head1 NAME -eForge - The great new eForge! +eForge::eForge - Interface with the DB and various other common functions for eForge =head1 VERSION Version 0.01 +=head1 LICENCE AND COPYRIGHT + +Copyright (C) [2014-2015] EMBL - European Bioinformatics Institute and University College London + +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation; version 2 dated June, 1991 or at your option +any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +A copy of the GNU General Public License is available in the source tree; +if not, write to the Free Software Foundation, Inc., +51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + +=head1 CONTACT + +Charles Breeze <c.breeze@ucl.ac.uk> + +Javier Herrero <javier.herrero@ucl.ac.uk> + =cut my $MAX_SQL_VARIABLES = 999; @@ -432,39 +456,4 @@ Assign any maf, gc, tss values to the percentile bins # return ($i, $j, $k); # } -=head1 AUTHOR - -Charles Breeze, C<< <c.breeze at ucl.ac.uk> >> - -=head1 SUPPORT - -You can find documentation for this module with the perldoc command. - - perldoc eForge - - -=head1 ACKNOWLEDGEMENTS - - -=head1 LICENSE AND COPYRIGHT - -Copyright 2015 Charles Breeze. - -This program is free software; you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation; version 2 dated June, 1991 or at your option -any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -A copy of the GNU General Public License is available in the source tree; -if not, write to the Free Software Foundation, Inc., -51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA - - -=cut - 1; diff --git a/eForge/ePlot.pm b/eForge/ePlot.pm index b95aa1f..f35dfaf 100644 --- a/eForge/ePlot.pm +++ b/eForge/ePlot.pm @@ -13,6 +13,30 @@ eForge::ePlot - Plotting utilities for eForge Version 0.01 +=head1 LICENCE AND COPYRIGHT + +Copyright (C) [2014-2015] EMBL - European Bioinformatics Institute and University College London + +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation; version 2 dated June, 1991 or at your option +any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +A copy of the GNU General Public License is available in the source tree; +if not, write to the Free Software Foundation, Inc., +51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + +=head1 CONTACT + +Charles Breeze <c.breeze@ucl.ac.uk> + +Javier Herrero <javier.herrero@ucl.ac.uk> + =cut our $VERSION = '0.01'; @@ -326,49 +350,4 @@ dt\$save('$chart', cdn = F)\n"; } } - -=head1 AUTHOR - -Charles Breeze, C<< <c.breeze at ucl.ac.uk> >> - -=head1 BUGS - -Please report any bugs or feature requests to C<bug-eforge at rt.cpan.org>, or through -the web interface at L<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=eForge>. I will be notified, and then you'll -automatically be notified of progress on your bug as I make changes. - - - - -=head1 SUPPORT - -You can find documentation for this module with the perldoc command. - - perldoc eForge::ePlot - - -=head1 ACKNOWLEDGEMENTS - - -=head1 LICENSE AND COPYRIGHT - -Copyright 2015 Charles Breeze. - -This program is free software; you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation; version 2 dated June, 1991 or at your option -any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -A copy of the GNU General Public License is available in the source tree; -if not, write to the Free Software Foundation, Inc., -51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA - - -=cut - -1; # End of ePlot +1; diff --git a/eForge/eStats.pm b/eForge/eStats.pm index 14421ce..2a7beb6 100644 --- a/eForge/eStats.pm +++ b/eForge/eStats.pm @@ -6,12 +6,38 @@ use warnings FATAL => 'all'; =head1 NAME -eStats - Stats for use in eForge +eForge::eStats - Stats for use in eForge =head1 VERSION Version 0.01 +=head1 LICENCE AND COPYRIGHT + +eforge.pl Functional analysis of EWAS MVPs + +Copyright (C) [2014-2015] EMBL - European Bioinformatics Institute and University College London + +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation; version 2 dated June, 1991 or at your option +any later version. + +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +A copy of the GNU General Public License is available in the source tree; +if not, write to the Free Software Foundation, Inc., +51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + +=head1 CONTACT + +Charles Breeze <c.breeze@ucl.ac.uk> + +Javier Herrero <javier.herrero@ucl.ac.uk> + =cut our $VERSION = '0.01'; @@ -174,51 +200,4 @@ sub fdr{ } } - - - - -=head1 AUTHOR - -Charles Breeze, C<< <c.breeze at ucl.ac.uk> >> - -=head1 BUGS -#not yet implemented below, it refers to eForge but it is not yet implemented (for cpan) even for Forge -Please report any bugs or feature requests to C<bug-eforge at rt.cpan.org>, or through -the web interface at L<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=eForge>. I will be notified, and then you'll -automatically be notified of progress on your bug as I make changes. - - - - -=head1 SUPPORT - -You can find documentation for this module with the perldoc command. - - perldoc Forge::eStats - - - -=head1 ACKNOWLEDGEMENTS - - -=head1 LICENSE AND COPYRIGHT - -eForge::eStats.pm - -Copyright (C) 2015 EMBL - European Bioinformatics Institute and University College London - -This program is free software: you can redistribute it and/or modify it under the terms of -the GNU General Public License as published by the Free Software Foundation, either version 3 -of the License, or (at your option) any later version. This program is distributed in the hope -that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY -or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Neither -the institution name nor the name eforge.pl can be used to endorse or promote products derived from -this software without prior written permission. For written permission, please contact -c.breeze@ucl.ac.uk . Products derived from this software may not be called eforge.pl nor may eforge.pl -appear in their names without prior written permission of the developers. You should have received -a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/. - -=cut - -1; # End of eStats +1; diff --git a/eforge.pl b/eforge.pl index a09c517..3d34e0f 100644 --- a/eforge.pl +++ b/eforge.pl @@ -125,31 +125,32 @@ =head1 OPTIONS =back -=head1 LICENCE +=head1 LICENCE AND COPYRIGHT eforge.pl Functional analysis of EWAS MVPs -Copyright (C) 2015 EMBL - European Bioinformatics Institute and University College London +Copyright (C) [2014-2015] EMBL - European Bioinformatics Institute and University College London -This program is free software: you can redistribute it and/or modify it under the terms of -the GNU General Public License as published by the Free Software Foundation, either version 3 -of the License, or (at your option) any later version. This program is distributed in the hope -that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY -or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Neither -the institution name nor the name eforge.pl can be used to endorse or promote products derived from -this software without prior written permission. For written permission, please contact -c.breeze@ucl.ac.uk. Products derived from this software may not be called eforge.pl nor may eforge.pl -appear in their names without prior written permission of the developers. You should have received -a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/. +This program is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation; version 2 dated June, 1991 or at your option +any later version. -=head1 AUTHOR +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. -Charles Breeze, UCL and EBI +A copy of the GNU General Public License is available in the source tree; +if not, write to the Free Software Foundation, Inc., +51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA =head1 CONTACT Charles Breeze <c.breeze@ucl.ac.uk> +Javier Herrero <javier.herrero@ucl.ac.uk> + =cut use strict; From d61058b1ef43456a6a5eb7ec0b0c8f645f86b8a3 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Wed, 30 Sep 2015 07:17:14 +0100 Subject: [PATCH 07/26] New DB schema - both code and DB are data-agnostic --- eForge/eForge.pm | 351 ++++++++++++++++++++++++++++----------------- eForge/ePlot.pm | 32 +++-- eForge/eStats.pm | 19 +-- eforge.pl | 127 +++++++++++----- webserver/INSTALL | 61 ++++---- webserver/cgi-bin/index.pl | 55 +++++-- 6 files changed, 416 insertions(+), 229 deletions(-) diff --git a/eForge/eForge.pm b/eForge/eForge.pm index 34e729f..2e2a571 100644 --- a/eForge/eForge.pm +++ b/eForge/eForge.pm @@ -1,10 +1,5 @@ package eForge::eForge; -use 5.010; -use strict; -use warnings FATAL => 'all'; -use Storable; - =head1 NAME eForge::eForge - Interface with the DB and various other common functions for eForge @@ -33,18 +28,28 @@ if not, write to the Free Software Foundation, Inc., =head1 CONTACT -Charles Breeze <c.breeze@ucl.ac.uk> +Charles Breeze, C<< <c.breeze at ucl.ac.uk> >> + +Javier Herrero, C<< <javier.herrero at ucl.ac.uk> >> -Javier Herrero <javier.herrero@ucl.ac.uk> +=head1 ACKNOWLEDGEMENTS + +This software is based on the FORGE tool developed by Ian Dunham at the EMBL-EBI =cut +use 5.010; +use strict; +use warnings FATAL => 'all'; +use Storable; + + my $MAX_SQL_VARIABLES = 999; our $VERSION = '0.01'; our (@ISA, @EXPORT); use Exporter; @ISA = qw(Exporter); -@EXPORT = qw(process_file match process_bits get_bits fetch_rsid fetch_loc get_cells assign bkgrdstat prox_filter); +@EXPORT = qw(get_all_datasets get_all_arrays get_all_proxy_filters process_file match process_bits get_bits get_cells assign bkgrdstat prox_filter); =head1 SYNOPSIS @@ -52,12 +57,13 @@ Provide functional modules for eForge =head1 EXPORT +get_all_datasets +get_all_arrays +get_all_proxy_filters process_file match process_bits get_bits -fetch_rsid -fetch_loc get_cells assign bkgrdstat @@ -91,14 +97,24 @@ sub bkgrdstat{ say $bfh join("\t", $flag, "cpg_island_relationship", @cpg_island_relationship); } + =head2 process_file -Processes various file formats. + Arg[1] : FILEHANDLE $input_fh + Arg[2] : string $format + Arg[3] : DB-connection-handle $dbh + Arg[4] : string $bkgd + Arg[5] : numeric $filter + Returns : arrayref of $probe_ids (string) + Example : my $probe_ids = process_file($fh, "probeid", $dbh, '450k', undef); + Description : Reads the list of probe IDs or locations from the file. If the file contains + locations, these will be translated into probe_ids + Exceptions : =cut sub process_file { - my ($fh, $format, $dbh, $filter) = @_; + my ($fh, $format, $dbh, $bkgd, $filter) = @_; my $probe_ids = []; if ($format =~ /^probe/i) { @@ -117,28 +133,27 @@ sub process_file { } } elsif ($format =~ /^bed/i) { + my $locations = []; while (<$fh>) { next if /^track/; chomp; - my ($chr, $beg, $end) = split "\t", $_; - next if (!defined($end)); + my ($chr, $from, $to) = split "\t", $_; + next if (!defined($to)); unless ($chr =~ /^chr/){ $chr = "chr". $chr; } - my $loc = "$chr:$beg-$beg"; - #get the $probe_id from the db - my $probe_id = fetch_probe_id($dbh, $loc); - push @$probe_ids, $probe_id if defined $probe_id; + push(@$locations, [$chr, $from]); } + $probe_ids = fetch_all_probe_ids($dbh, $bkgd, $locations); } elsif ($format =~ /^tabix/i) { + my $locations = []; while (<$fh>) { chomp; - my $loc = $_; - #get the $probe_id from the db - my $probe_id = fetch_probe_id($dbh, $loc); - push @$probe_ids, $probe_id if defined $probe_id; + my ($chr, $from, $to) = $_ =~ /(.+)\:(\d+)\-(\d+)/; + push(@$locations, [$chr, $from]); } + $probe_ids = fetch_all_probe_ids($dbh, $bkgd, $locations); } return $probe_ids; } @@ -236,51 +251,154 @@ sub match{ =head2 process_bits -Processes bitstrings to get a count of overlaps for each cell type. + Arg[1] : arrayref of arrays $rows ($probe_id, $sum, $bit_string, $feature, $CGI_context) + Arg[2] : arrayref of strings $cells (shortname for the cells in the dataset) + Arg[3] : string $dataset + Returns : hashref $stats + Example : my $result = process_bits($rows, $cells, 'erc'); + Description : Returns a reference to a complex hash with stats from the rows. These are split + into 'MVPS' and 'CELLS'. The former contains 'SUM' and 'PARAMS' for each probe ID + while the latter contains 'COUNT' and 'MVPS' for each cell. + Exceptions : Dies if the number of cells does not match the length of the bit string. =cut -sub process_bits{ +sub process_bits { my ($rows, $cells, $data) = @_; my %test; my @test_cells; my @indexes = 0..(@$cells-1); foreach my $row (@{$rows}){ - my ($location, $probeid, $sum, $bit_string, $feature, $cpg_island_relationship); - if ($data eq "erc"){ - ($location, $probeid, undef, undef, $bit_string, $sum, undef, undef, undef, undef, $feature, $cpg_island_relationship) = @$row; - } - elsif ($data eq "encode"){ - ($location, $probeid, $bit_string, $sum, undef, undef, undef, undef, undef, undef, $feature, $cpg_island_relationship) = @$row; - } - elsif ($data eq "blueprint"){ - ($location, $probeid, undef, undef, undef, undef, $bit_string, $sum, undef, undef, $feature, $cpg_island_relationship) = @$row; - } - elsif ($data eq "erc2"){ - ($location, $probeid, undef, undef, undef, undef, undef, undef, $bit_string, $sum, $feature, $cpg_island_relationship) = @$row; - } + my ($probeid, $sum, $bit_string, $feature, $cpg_island_relationship) = @$row; $test{'MVPS'}{$probeid}{'SUM'} = $sum; $test{'MVPS'}{$probeid}{'PARAMS'} = join("\t", $feature, $cpg_island_relationship); - die if (scalar(@$cells) ne length($bit_string)); + die "For $data, found ".scalar(@$cells)." cells for ".length($bit_string)." bits\n" if (scalar(@$cells) ne length($bit_string)); foreach my $index (@indexes) { ## $bit_string is a string made of 0s and 1s. If it is a 1 for this position, count and push if (substr($bit_string, $index, 1)) { $test_cells[$index][0]++; push @{$test_cells[$index][1]}, $probeid; } - } - } + } + } my $index = 0; foreach my $cell (@$cells){ $test{'CELLS'}{$cell}{'COUNT'} = $test_cells[$index][0] if ($test_cells[$index][0]); $test{'CELLS'}{$cell}{'MVPS'} = $test_cells[$index][1] if ($test_cells[$index][1]); $index++; - } + } return \%test; - } +} +=head2 get_all_datasets + + Arg[1] : DB-handle $dbh + Arg[2] : (optional) string $species_name + Returns : arrayref of hashes (tag/name) + Example : my $all_datasets = get_all_dataset($dbh); + Description : Returns the list of all datasets in the DB. It returns an arrayref of hashes. Each + hash has two keys: 'tag' (string ID of the dataset) and 'name' (full name). You + can limit the dataset to the ones available for a given species. + Exceptions : + +=cut + +sub get_all_datasets { + my ($dbh, $species_name) = @_; + my $datasets; + + my $sql = "SELECT dataset_tag, dataset_name FROM dataset ORDER BY dataset_id"; + my @bind_params = (); + if ($species_name) { + $sql .= " WHERE species_name = ?"; + push(@bind_params, $species_name); + } + my ($tag, $name); + my $sth = $dbh->prepare($sql); + $sth->execute(@bind_params); + $sth->bind_columns(\$tag, \$name); + while ($sth->fetch) { + push(@$datasets, {tag => $tag, name => $name}); + } + + return($datasets); +} + + +=head2 get_all_arrays + + Arg[1] : DB-handle $dbh + Arg[2] : (optional) string $species_name + Returns : arrayref of hashes (tag/name) + Example : my $all_arrays = get_all_arrays($dbh); + Description : Returns the list of all arrays in the DB. It returns an arrayref of hashes. Each + hash has two keys: 'tag' (string ID of the array) and 'name' (full name). You + can limit the arrays to the ones available for a given species. + Exceptions : + +=cut + +sub get_all_arrays { + my ($dbh, $species_name) = @_; + my $arrays; + + my $sql = "SELECT array_tag, array_name FROM array order by array_id"; + my @bind_params = (); + if ($species_name) { + $sql .= " WHERE species_name = ?"; + push(@bind_params, $species_name); + } + my ($tag, $name); + my $sth = $dbh->prepare($sql); + $sth->execute(); + $sth->bind_columns(\$tag, \$name); + while ($sth->fetch) { + push(@$arrays, {tag => $tag, name => $name}); + } + + return($arrays); +} + + +=head2 get_all_proxy_filters + + Arg[1] : DB-handle $dbh + Arg[2] : (optional) string $bkgd + Returns : hashref of proxy-filters (string) + Example : my $proxy_filters = get_all_proxy_filters($dbh, '450k'); + Description : Returns the list of proxy filters available in the DB. It returns a hashref whose + keys are the bkgd names (i.e. array tags) and values are the name of the proxy + filter. At the moment the schema supports just one proxy filter per array. + If you provide a $bkgd, the result will be limited to that array. Note that you + will still get a hashref with exactly the same structure. Only the content will + be limited. + Exceptions : + +=cut + +sub get_all_proxy_filters { + my ($dbh, $array_tag) = @_; + my $proxy_filters; + + my $sql = "SELECT array_tag, description FROM proxy_filter_info JOIN array USING (array_id)"; + my @bind_params = (); + if ($array_tag) { + $sql .= " WHERE array_tag = ?"; + push(@bind_params, $array_tag); + } + my ($this_array_tag, $description); + my $sth = $dbh->prepare($sql); + $sth->execute(); + $sth->bind_columns(\$this_array_tag, \$description); + while ($sth->fetch) { + $proxy_filters->{$this_array_tag} = $description; + } + + return($proxy_filters); +} + =head2 get_bits Get the bitstrings for an array of mvps from the sqlite db @@ -288,8 +406,7 @@ Get the bitstrings for an array of mvps from the sqlite db =cut sub get_bits{ - - my ($mvps, $dbh) = @_; + my ($dbh, $dataset_tag, $array_tag, $mvps) = @_; my @results; for (my $loop = 0; $loop * $MAX_SQL_VARIABLES < @$mvps; $loop++) { @@ -297,43 +414,59 @@ sub get_bits{ my $end = ($loop + 1) * $MAX_SQL_VARIABLES - 1; $end = @$mvps -1 if ($end >= @$mvps); - my $sql = "SELECT * FROM bits WHERE probeid IN (?". (",?" x ($end - $start)).")"; + my $sql = "SELECT probe_id, sum, bit, gene_group, cgi_group + FROM probe_annotation + JOIN probe_bitstring USING (array_id, probe_id) + JOIN dataset USING (dataset_id) + JOIN array USING (array_id) + WHERE array_tag = ? and dataset_tag = ? + AND probe_id IN (?". (",?" x ($end - $start)).")"; my $sth = $dbh->prepare_cached($sql); #get the blocks form the ld table - $sth->execute(@$mvps[$start..$end]); + $sth->execute($array_tag, $dataset_tag, @$mvps[$start..$end]); while (my $row = $sth->fetchrow_arrayref()) { - push @results, [@$row]; + push @results, [@$row]; } $sth->finish(); - } + } return \@results;# return the bitstring line from the database - } +} + -=head2 fetch_rsid +=head2 fetch_all_probe_ids -gets the rsid for a SNP where a location is given. + Arg[1] : DB-handle $dbh + Arg[2] : string $bkgd + Arg[3] : arrayref of locations [$chr, $pos] + Returns : arrayref of probe IDs (string) + Description : Given a list of chromosome names and location pairs, the method fetches the name + of the probe ID for that location. To do this successfully, this method requires + to know the background (i.e. array) you want to translate the locations to. + Exceptions : =cut -sub fetch_probe_id { +sub fetch_all_probe_ids { #gets the rsid for a SNP where a location is given - my ($dbh, $loc) = @_; + my ($dbh, $bkgd, $locations) = @_; - my $sth = $dbh->prepare_cached("SELECT probeid FROM bits WHERE location = ?"); + my $sth = $dbh->prepare("SELECT probe_id + FROM probe_mapping + WHERE chr_name = ? AND position = ?"); + my $probe_ids = []; - $sth->execute($loc); - my $result = $sth->fetchall_arrayref(); - my $probe_id; - foreach my $row (@{$result}) { - $probe_id = $$row[0]; + foreach my $this_loc (@$locations) { + my ($chr, $pos) = @$this_loc; + $sth->execute($chr, $pos); + my $result = $sth->fetchall_arrayref(); + my $probe_id; + foreach my $row (@{$result}) { + push(@$probe_ids, $$row[0]); + } } $sth->finish(); - if (defined $probe_id && $probe_id =~ /^cg\d+/) { - return $probe_id; - } else { - return "no PROBEID match for $loc"; - } + return $probe_ids; } =head2 prox_filter @@ -355,7 +488,7 @@ sub prox_filter{ my $end = ($loop + 1) * $MAX_SQL_VARIABLES - 1; $end = @$mvps -1 if ($end >= @$mvps); - my $sql = "SELECT probeid,proxy_probes FROM proxy_filter WHERE probeid IN (?". (",?" x ($end - $start)).")"; + my $sql = "SELECT probe_id,proxy_probes FROM proxy_filter WHERE probe_id IN (?". (",?" x ($end - $start)).")"; my $sth = $dbh->prepare($sql); #get the blocks form the ld table $sth->execute(@$mvps[$start..$end]); my $result = $sth->fetchall_arrayref(); @@ -377,83 +510,33 @@ sub prox_filter{ return (\%prox_excluded, @mvps_filtered); } - =head2 get_cells Read the correct cell list based on data (erc, erc2, blueprint or encode). Also gets the tissue names for the cells. =cut -sub get_cells{ - # read the correct cell list based on data (erc, erc2, blueprint or encode). Also gets the tissue names for the cells. - my ($data, $dbh) = @_; - - my $table = "cells_".$data; - - # Check that the table exists in the DB (note, some magic here that might be SQLite-specific) - my @tables = grep {/^cells_/} map {$_ =~ s/"//g; $_ =~ s/^main\.//; $_} $dbh->tables(); - if (!grep {/$table/} @tables) { - die "The database does not contain information for the data background provided.\n"; +sub get_cells { + my ($dataset_tag, $dbh) = @_; + my $samples; + + my $sth = $dbh->prepare("SELECT shortcell, tissue, datatype, file, acc FROM dataset JOIN sample USING (dataset_id) WHERE dataset_tag = ? ORDER BY sample_order"); + $sth->execute($dataset_tag); + my ($shortcell, $tissue, $datatype, $file, $acc); + $sth->bind_columns(\$shortcell, \$tissue, \$datatype, \$file, \$acc); + my ($cells, $tissues); + while ($sth->fetch) { + $shortcell = "$shortcell|$file"; # Sometimes the same cell is used twice, with a differnt file so need to record separately (e.g. WI-38). + push @$cells, $shortcell; + $$tissues{$shortcell}{'tissue'} = $tissue; # this is the hash that is used to connect cells and tissues and ultimately provide the sorting order + $$tissues{$shortcell}{'datatype'} = $datatype; + $$tissues{$shortcell}{'file'} = $file; + $$tissues{$shortcell}{'acc'} = $acc; } +# use Data::Dumper; +# print Dumper %$tissues; - my $sth = $dbh->prepare("SELECT shortcell,tissue,file,acc FROM $table"); - $sth->execute(); - my $ver = $sth->fetchall_arrayref(); - $sth->finish(); - my ($cells, $tissues, $acc); - foreach my $row (@$ver){ - my $cell = shift @$row; - my $tissue = shift @$row; - my $file = shift @$row; - my $acc = shift @$row; - $cell = "$cell|$file"; # Sometimes the same cell is used twice, with a differnt file so need to record separately (e.g. WI-38). - push @$cells, $cell; - $$tissues{$cell}{'tissue'} = $tissue; # this is the hash that is used to connect cells and tissues and ultimately provide the sorting order - $$tissues{$cell}{'file'} = $file; - $$tissues{$cell}{'acc'} = $acc; - } - #print Dumper %$tissues; return ($cells, $tissues); # return - } - -=head2 assign - -Assign any maf, gc, tss values to the percentile bins - -=cut - -#sub assign{ -# #sub routine to assign any maf, gc, tss values to the percentile bins -# my ($gc, $tss, $maf, $params) = @_; -# my ($i, $j, $k); -# my $n = 1; -# foreach my $pc (@{$$params{'gc'}}){ -# if ($gc <= $pc) { -# $i = $n; -# } -# else{ -# $n++; -# } -# } -# $n=1; -# foreach my $pc (@{$$params{'tss'}}){ -# if ($tss <= $pc) { -# $j = $n; -# } -# else{ -# $n++; -# } -# } -# $n=1; -# foreach my $pc (@{$$params{'maf'}}){ -# if ($maf <= $pc) { -# $k = $n; -# } -# else{ -# $n++; -# } -# } -# return ($i, $j, $k); -# } +} 1; diff --git a/eForge/ePlot.pm b/eForge/ePlot.pm index f35dfaf..be0236a 100644 --- a/eForge/ePlot.pm +++ b/eForge/ePlot.pm @@ -1,10 +1,5 @@ package eForge::ePlot; -use 5.010; -use strict; -use warnings FATAL => 'all'; -use Sort::Naturally; - =head1 NAME eForge::ePlot - Plotting utilities for eForge @@ -33,12 +28,21 @@ if not, write to the Free Software Foundation, Inc., =head1 CONTACT -Charles Breeze <c.breeze@ucl.ac.uk> +Charles Breeze, C<< <c.breeze at ucl.ac.uk> >> + +Javier Herrero, C<< <javier.herrero at ucl.ac.uk> >> + +=head1 ACKNOWLEDGEMENTS -Javier Herrero <javier.herrero@ucl.ac.uk> +This software is based on the FORGE tool developed by Ian Dunham at the EMBL-EBI =cut +use 5.010; +use strict; +use warnings FATAL => 'all'; +use Sort::Naturally; + our $VERSION = '0.01'; our (@ISA, @EXPORT, @EXPORT_OK); @@ -164,6 +168,14 @@ results\$Class <- cut(results\$Pvalue, breaks =c(0, $t2, $t1, 1)/length(unique(r # Class splits the data into non-significant, marginally significant and significant according to q-value (B-Y FDR adjusted) results\$Class2 <- cut(results\$Qvalue, breaks =c(0, $t2, $t1, 1), labels=FALSE, include.lowest=TRUE) +color.axis.palette = c(); +if (length(which(results\$Class2 == 1)) > 0 ) { + color.axis.palette = c('red'); +} +if (length(which(results\$Class2 == 2)) > 0 ) { + color.axis.palette = c(color.axis.palette, 'pink'); +} +color.axis.palette = c(color.axis.palette, 'lightblue', 'lightblue'); # Add it twice to force the color if only non-significant values results\$log10pvalue <- -log10(results\$Pvalue) @@ -191,7 +203,7 @@ bounds.width=dplot.width - bounds.x - 20 d1 <- dPlot( y = 'log10pvalue', x = c('TissueCell'), - groups = c('TissueCell', 'Accession', 'Pvalue', 'Qvalue', 'Probe'), + groups = c('TissueCell', 'Accession', 'Pvalue', 'Qvalue', 'Datatype', 'Probe'), data = results, type = 'bubble', width = dplot.width, @@ -210,7 +222,7 @@ d1\$yAxis( type = 'addMeasureAxis' ) d1\$colorAxis( type = 'addColorAxis', colorSeries = 'Class2', - palette = c('red', 'pink', 'lightblue')) + palette = color.axis.palette) # Builds a JS string to add labels for tissues labels.string = paste(paste0(\" @@ -322,7 +334,7 @@ sub table{ open my $rcfh, ">", $rfile; print $rcfh "setwd('$Rdir') results <- read.table('$filename', header = TRUE, sep='\\t') -results <- subset(results, T, select = c('Cell', 'Tissue', 'Accession', 'Pvalue', 'Qvalue', 'Probe')) +results <- subset(results, T, select = c('Cell', 'Tissue', 'Datatype', 'Accession', 'Pvalue', 'Qvalue', 'Probe')) require(rCharts) dt <- dTable( results, diff --git a/eForge/eStats.pm b/eForge/eStats.pm index 2a7beb6..ca6334d 100644 --- a/eForge/eStats.pm +++ b/eForge/eStats.pm @@ -1,9 +1,5 @@ package eForge::eStats; -use 5.010; -use strict; -use warnings FATAL => 'all'; - =head1 NAME eForge::eStats - Stats for use in eForge @@ -14,8 +10,6 @@ Version 0.01 =head1 LICENCE AND COPYRIGHT -eforge.pl Functional analysis of EWAS MVPs - Copyright (C) [2014-2015] EMBL - European Bioinformatics Institute and University College London This program is free software; you can redistribute it and/or modify @@ -34,12 +28,21 @@ if not, write to the Free Software Foundation, Inc., =head1 CONTACT -Charles Breeze <c.breeze@ucl.ac.uk> +Charles Breeze, C<< <c.breeze at ucl.ac.uk> >> + +Javier Herrero, C<< <javier.herrero at ucl.ac.uk> >> -Javier Herrero <javier.herrero@ucl.ac.uk> +=head1 ACKNOWLEDGEMENTS + +This software is based on the FORGE tool developed by Ian Dunham at the EMBL-EBI =cut + +use 5.010; +use strict; +use warnings FATAL => 'all'; + our $VERSION = '0.01'; our (@ISA, @EXPORT); diff --git a/eforge.pl b/eforge.pl index 3d34e0f..1a53a9c 100644 --- a/eforge.pl +++ b/eforge.pl @@ -37,6 +37,8 @@ =head1 OPTIONS Dataset to analyse. Either ENCODE data ('encode'), unconsolidated Roadmap Epigenome data ('erc'), consolidated Roadmap Epigenome data ('erc2'), or Blueprint data ('blueprint'). erc by default. +Use -data ? to get a list of available datasets on your local install. + =item B<peaks> Use peaks instead of hotspots. Peaks are more stringent DNase1 peaks calls representing DNase hypersensitive sites, @@ -48,6 +50,8 @@ =head1 OPTIONS For the time being, it is suficient for MVPs to be on the 450k array. Probes within 1kb of each other will undergo filtering. +Use -bkgd ? to get a list of available backgrounds on your local install. + =item B<label> Supply a label that you want to use for the plotting titles, and filenames. @@ -147,7 +151,13 @@ =head1 LICENCE AND COPYRIGHT =head1 CONTACT -Charles Breeze <c.breeze@ucl.ac.uk> +Charles Breeze, C<< <c.breeze at ucl.ac.uk> >> + +Javier Herrero, C<< <javier.herrero at ucl.ac.uk> >> + +=head1 ACKNOWLEDGEMENTS + +This software is based on the FORGE tool developed by Ian Dunham at the EMBL-EBI Javier Herrero <javier.herrero@ucl.ac.uk> @@ -175,12 +185,8 @@ =head1 CONTACT my $dbname = "eforge_1.1.db"; -my $bkgd_label = { - '450k' => 'Illumina Infinium HumanMethylation450 BeadChip', - '27k' => 'Illumina Infinium HumanMethylation27 BeadChip (450k array subset)', - }; - -my $bkgd = '450k'; # Default value +my $bkgd; # Default value +my $bkgd_label; my ($data, $peaks, $label, $file, $format, $min_mvps, $bkgrdstat, $noplot, $reps, $help, $man, $thresh, $proxy, $noproxy, $depletion, $filter, $out_dir, @mvplist, $web, $autoopen); @@ -224,19 +230,83 @@ =head1 CONTACT $min_mvps = 5; } -# define which data we are dealing with for the bitstrings, erc, erc2, blueprint or encode -unless (defined $data ) { - $data = "erc"; -} - # Label for plots unless (defined $label) { $label = "No label given"; } -if (!grep {$bkgd =~ /^$_/i and $bkgd = $_} keys %$bkgd_label) { - die "Background (--bkgd) must be one of: ".join(", ", keys %$bkgd_label)."\n"; +## ============================================================================ +## Connect to the DB +## ============================================================================ +# This reads the config file and sets up the $datadir variable +my $dirname = dirname(__FILE__); +my $cfg = Config::IniFiles->new( -file => "$dirname/eforge.ini" ); +my $datadir = $cfg->val('Files', 'datadir'); + +unless (-s "$datadir/$dbname") { + die "Database $dbname not found or empty"; +} +my $dsn = "dbi:SQLite:dbname=$datadir/$dbname"; +my $dbh = DBI->connect($dsn, "", "") or die $DBI::errstr; +## ============================================================================ + + +## ============================================================================ +## Check the dataset against the info on the DB +## ============================================================================ +my $all_datasets = get_all_datasets($dbh); +if (!defined($all_datasets)) { + die "Empty database: no dataset loaded!\n"; +} elsif (!defined($data)) { + $data = $all_datasets->[0]->{tag}; + print "Using default dataset: [$data] ".$all_datasets->[0]->{name}."\n"; +} elsif ($data eq "?") { + print "Available datasets:\n - [".join("\n - [", map {$_->{tag}."] ".$_->{name}} @$all_datasets)."\n"; + exit(); +} elsif (!grep {$_ eq $data} map {$_->{tag}} @$all_datasets) { + die "Dataset $data unknown\nAvailable datasets:\n - [".join("\n - [", map {$_->{tag}."] ".$_->{name}} @$all_datasets)."\n"; } +## ============================================================================ + + +## ============================================================================ +## Check the array name (A.K.A. background) against DB +## ============================================================================ +my $all_arrays = get_all_arrays($dbh); +if (!defined($all_arrays)) { + die "Empty database: no background loaded!\n"; +} elsif (!defined($bkgd)) { + $bkgd = $all_arrays->[0]->{tag}; + print "Using default background: [$bkgd] ".$all_arrays->[0]->{name}."\n"; + $bkgd_label = $all_arrays->[0]->{name}; +} elsif ($bkgd eq "?") { + print "Available arrays:\n - [".join("\n - [", map {$_->{tag}."] ".$_->{name}} @$all_arrays)."\n"; + exit(); +} elsif (!grep {$_ eq $bkgd} map {$_->{tag}} @$all_arrays) { + die "Array $bkgd unknown\nAvailable arrays:\n - [".join("\n - [", map {$_->{tag}."] ".$_->{name}} @$all_arrays)."\n"; +} else { + foreach my $this_array (@$all_arrays) { + if ($this_array->{tag} eq $bkgd) { + $bkgd_label = $this_array->{name}; + last; + } + } +} +## ============================================================================ + + +## ============================================================================ +## Check the proxy_filter (A.K.A. filter) against DB +## ============================================================================ +# Set proximity filter +unless (defined $noproxy) { + my $all_proxy_filters = get_all_proxy_filters($dbh); + if ($all_proxy_filters->{$bkgd}) { + $proxy = $all_proxy_filters->{$bkgd}; + } +} +## ============================================================================ + if (defined $depletion) { $label = "$label.depletion"; @@ -245,16 +315,13 @@ =head1 CONTACT #regexp puts underscores where labels before (my $lab = $label) =~ s/\s/_/g; $lab = "$lab.$bkgd.$data"; + #format for reading from file unless (defined $format) { $format = 'probeid'; } -# Read the config file, eforge.ini -my $dirname = dirname(__FILE__); -my $cfg = Config::IniFiles->new( -file => "$dirname/eforge.ini" ); -my $datadir = $cfg->val('Files', 'datadir'); @@ -282,18 +349,6 @@ =head1 CONTACT $t2 = 0.01; } -# Set proximity filter -unless (defined $noproxy) { - $proxy="1 kb"; -} - - -unless (-s "$datadir/$dbname") { - die "Database $dbname not found or empty"; -} -my $dsn = "dbi:SQLite:dbname=$datadir/$dbname"; -my $dbh = DBI->connect($dsn, "", "") or die $DBI::errstr; - # mvps need to come either from a file or a list my $mvps; @@ -309,7 +364,7 @@ =head1 CONTACT } } open my $fh, "<", $file or die "cannot open file $file : $!"; - $mvps = process_file($fh, $format, $dbh, $filter); + $mvps = process_file($fh, $format, $dbh, $bkgd, $filter); } elsif (@mvplist) { @$mvps = split(/,/,join(',',@mvplist)); @@ -363,7 +418,7 @@ =head1 CONTACT my ($cells, $tissues) = get_cells($data, $dbh); # get the bit strings for the test mvps from the database file -my $rows = get_bits($mvps, $dbh); +my $rows = get_bits($dbh, $data, $bkgd, $mvps); # unpack the bitstrings and store the overlaps by cell. my $test = process_bits($rows, $cells, $data); @@ -390,7 +445,7 @@ =head1 CONTACT } if (scalar @missing > 0) { - warn "The following " . scalar @missing . " MVPs have not been analysed because they were not found on the ".$bkgd_label->{$bkgd}."\n"; + warn "The following " . scalar @missing . " MVPs have not been analysed because they were not found on the ".$bkgd_label."\n"; warn join("\n", @missing) . "\n"; } if (defined $proxy) { @@ -426,7 +481,7 @@ =head1 CONTACT foreach my $bkgrd (keys %{$picks}) { warn "[".scalar(localtime())."] Repetition $num out of ".$reps."\n" if (++$num%100 == 0); #$rows = get_bits(\@{$$picks{$bkgrd}}, $sth); - $rows = get_bits(\@{$$picks{$bkgrd}}, $dbh); + $rows = get_bits($dbh, $data, $bkgd, \@{$$picks{$bkgrd}}); $backmvps += scalar @$rows; #$backmvps is the total number of background probes analysed unless (scalar @$rows == scalar @foundmvps) { warn "Background " . $bkgrd . " only " . scalar @$rows . " probes out of " . scalar @foundmvps . "\n"; @@ -500,7 +555,7 @@ =head1 CONTACT # This gives the list of overlapping MVPs for use in the tooltips. If there are a lot of them this can be a little useless my ($shortcell, undef) = split('\|', $cell); # undo the concatenation from earlier to deal with identical cell names. - push(@results, [$zscore, $pbinom, $shortcell, $$tissues{$cell}{'tissue'}, $$tissues{$cell}{'file'}, $mvp_string, $$tissues{$cell}{'acc'}]); + push(@results, [$zscore, $pbinom, $shortcell, $$tissues{$cell}{'tissue'}, $$tissues{$cell}{'datatype'}, $$tissues{$cell}{'file'}, $mvp_string, $$tissues{$cell}{'acc'}]); } close($bfh); @@ -511,7 +566,7 @@ =head1 CONTACT # Write the results to a tab-separated file my $filename = "$lab.chart.tsv"; open my $ofh, ">", "$out_dir/$filename" or die "Cannot open $out_dir/$filename: $!"; -print $ofh join("\t", "Zscore", "Pvalue", "Cell", "Tissue", "File", "Probe", "Accession", "Qvalue"), "\n"; +print $ofh join("\t", "Zscore", "Pvalue", "Cell", "Tissue", "Datatype", "File", "Probe", "Accession", "Qvalue"), "\n"; for (my $i = 0; $i < @results; $i++) { print $ofh join("\t", @{$results[$i]}, $qvalues->[$i]), "\n"; } diff --git a/webserver/INSTALL b/webserver/INSTALL index 4020b69..8548b77 100644 --- a/webserver/INSTALL +++ b/webserver/INSTALL @@ -65,62 +65,71 @@ Check that these work. If the .dchart.html cannot be open. By default, the HTML location of the js code on the local machine. For the server, this should point at a public URL server by the server itself. -3. Install the Apache web browser ---------------------------------- +3. Install the web server +------------------------- -3.a. Install the package: +3.a. Install the Apache package if required: sudo yum install httpd.x86_64 3.b. Create some directories for hosting the code, log and result files: - sudo mkdir /var/www/eFORGE/ - cd /var/www/eFORGE/ + sudo mkdir /var/www/eFORGE.v1.1/ + cd /var/www/eFORGE.v1.1/ sudo mkdir -p bin log cgi-bin html html/files sudo chown apache log html/files # the user under which you run apache (see the line "User" in # /etc/httpd/conf/httpd.conf) 3.c. Copy the webserver files to the right directories - sudo rsync -avPL ~/eFORGE/webserver/cgi-bin/ /var/www/eFORGE/cgi-bin/ - sudo rsync -avPL ~/eFORGE/webserver/bin/ /var/www/eFORGE/bin/ - sudo rsync -avPL ~/eFORGE/webserver/html/ /var/www/eFORGE/html/ - sudo rsync -avPL ~/eFORGE/eforge.db /var/www/eFORGE/bin/ - sudo rsync -avPL ~/eFORGE/eforge_1.1.db /var/www/eFORGE/bin/ - sudo rsync -avPL ~/eFORGE/mvp_450k_bins /var/www/eFORGE/bin/ - sudo rsync -avPL ~/eFORGE/mvp_27k_bins /var/www/eFORGE/bin/ + sudo rsync -avPL ~/eFORGE/webserver/cgi-bin/ /var/www/eFORGE.v1.1/cgi-bin/ + sudo rsync -avPL ~/eFORGE/webserver/bin/ /var/www/eFORGE.v1.1/bin/ + sudo rsync -avPL ~/eFORGE/webserver/html/ /var/www/eFORGE.v1.1/html/ + sudo rsync -avPL ~/eFORGE/eforge.db /var/www/eFORGE.v1.1/bin/ + sudo rsync -avPL ~/eFORGE/eforge_1.1.db /var/www/eFORGE.v1.1/bin/ + sudo rsync -avPL ~/eFORGE/mvp_450k_bins /var/www/eFORGE.v1.1/bin/ + sudo rsync -avPL ~/eFORGE/mvp_27k_bins /var/www/eFORGE.v1.1/bin/ 3.e. Add links to the database files for the Downloads page: - cd /var/www/eFORGE/html/files + cd /var/www/eFORGE.v1.1/html/files sudo ln -s ../../bin/eforge.db . sudo ln -s ../../bin/eforge_1.1.db . sudo ln -s ../../bin/mvp_450k_bins . sudo ln -s ../../bin/mvp_27k_bins . -3.f. Configure the Apache server +3.f. Create the configuration files + +These files contain a list of arrays and dataset included in the database. They are used by the +web server to know what it can offer without having to query the DB every time. + + cd /var/www/eFORGE.v1.1/bin + perl eforge.pl -data ? > data.conf + perl eforge.pl -bkgd ? > bkgd.conf + +3.g. Configure the Apache server You can choose to either run eFORGE on a VirtualHost (like http://eforge.cs.ucl.ac.uk/) or on a folder (like http://blic.cs.ucl.ac.uk/eFORGE). OPTION 1 -- Configure an Apache VirtualHost for eFORGE: - cat > /etc/http/conf.d/eforge.conf + cat > /etc/http/conf.d/eforge.v1.1.conf <VirtualHost *:80> ServerName eforge.cs.ucl.ac.uk DocumentRoot /var/www/eFORGE/html - ScriptAlias /cgi-bin/ /var/www/eFORGE/cgi-bin/ + ScriptAlias /cgi-bin/ /var/www/eFORGE.v1.1/cgi-bin/ <IfModule dir_module> DirectoryIndex index.html /cgi-bin/index.pl </IfModule> - <Directory "/var/www/eFORGE/html"> + <Directory "/var/www/eFORGE.v1.1/html"> Order allow,deny Allow from all </Directory> - <Directory "/var/www/eFORGE/cgi-bin"> + <Directory "/var/www/eFORGE.v1.1/cgi-bin"> AllowOverride None Options None Order allow,deny @@ -131,18 +140,18 @@ OPTION 1 -- Configure an Apache VirtualHost for eFORGE: OPTION 2 -- Configure an Apache VirtualHost for eFORGE: - cat > /etc/http/conf.d/eforge.conf -ScriptAlias /eFORGE/cgi-bin/ /var/www/eFORGE/cgi-bin/ -Alias "/eFORGE" "/var/www/eFORGE/html" + cat > /etc/http/conf.d/eforge.v1.1.conf +ScriptAlias /eFORGE.v1.1/cgi-bin/ /var/www/eFORGE.v1.1/cgi-bin/ +Alias "/eFORGE.v1.1" "/var/www/eFORGE.v1.1/html" -<Directory "/var/www/eFORGE/html/"> +<Directory "/var/www/eFORGE.v1.1/html/"> Order allow,deny Allow from all DirectoryIndex index.html cgi-bin/index.pl </Directory> -<Directory "/var/www/eFORGE/cgi-bin/"> +<Directory "/var/www/eFORGE.v1.1/cgi-bin/"> AllowOverride None Options None Order allow,deny @@ -150,11 +159,11 @@ Alias "/eFORGE" "/var/www/eFORGE/html" </Directory> -3.g. Copy the rCharts libraries to the html path: +3.h. Copy the rCharts libraries to the html path: - sudo rsync -avP /usr/lib64/R/library/rCharts/libraries /var/www/eFORGE/html/ + sudo rsync -avP /usr/lib64/R/library/rCharts/libraries /var/www/eFORGE.v1.1/html/ -3.h Re-start Apache +3.i Re-start Apache sudo /etc/init.d/httpd restart diff --git a/webserver/cgi-bin/index.pl b/webserver/cgi-bin/index.pl index ba50234..c19de77 100755 --- a/webserver/cgi-bin/index.pl +++ b/webserver/cgi-bin/index.pl @@ -31,7 +31,7 @@ # Running on http://server.org/ -> $WEB_ROOT = "" # Running on http://server.org/tool/ -> $WEB_ROOT = "/tool" # IMPORTANT - DO NOT INCLUDE A TRAILING '/' -my $WEB_ROOT = ""; +my $WEB_ROOT = "/eFORGE.v1.1"; # The location of the files w.r.t. the base URL (DO NOT CHANGE) my $WEB_OUTDIR = "/files"; @@ -49,6 +49,10 @@ my $title = "eFORGE v1.1"; +my $bkgd_conf = read_conf_file("$BIN_DIR/bkgd.conf"); + +my $ref_data_conf = read_conf_file("$BIN_DIR/data.conf"); + my $breadcrumbs = [ {"UCL Cancer Institute" => "http://www.ucl.ac.uk/cancer"}, {"Cancer Biology" => "http://www.ucl.ac.uk/cancer/rescancerbiol/cancerbiology"}, @@ -63,6 +67,8 @@ {"Documentation" => "$WEB_ROOT/?documentation"}, {"Download" => "$WEB_ROOT/?download"}, {"About" => "$WEB_ROOT/?about"}, + {"__title__" => "Previous versions"}, + {"eFORGE v1.0" => "http://eforge.cs.ucl.ac.uk/eFORGE.v1.0"}, {"__title__" => "UCL Cancer Institute"}, {"Home" => "http://www.ucl.ac.uk/cancer/"}, {"Medical Genomics" => "http://www.ucl.ac.uk/cancer/medical-genomics/medgenhome"}, @@ -103,6 +109,29 @@ exit(0); +sub read_conf_file { + my ($file) = @_; + open(CONF, $file) or die; + my $default; + my $values; + my $labels; + while (<CONF>) { + chomp; + if (/ \- \[([^\]]+)\]\s+(.+)/) { + my $key = $1; + my $label = $2; + push(@$values, $key); + $labels->{$key} = $label; + } + } + close(CONF); + my $conf_hash = { + 'default' => $values->[0], + 'values' => $values, + 'labels' => $labels, + }; + return $conf_hash; +} =head2 get_outdir @@ -229,8 +258,7 @@ sub print_form { td(["Name (optional):", textfield('label', '', 58)]), td(["Platform:", - popup_menu('bkgd', ['450k', '27k'], '450k', {'450k'=>'Illumina 450K methylation array', - '27k'=>'Illumina 27k methylation array'})]), + popup_menu('bkgd', $bkgd_conf->{'values'}, $bkgd_conf->{'default'}, $bkgd_conf->{'labels'})]), th({-colspan=>2}, ["<hr>"]), @@ -239,13 +267,7 @@ sub print_form { ## ================================================================ th(["Analysis Options", ""]), td(["Analyse data from:", - radio_group('ref_data', ['erc2'], 'erc2', 'true', {'erc2'=>' Consolidated Roadmap Epigenomics'} )]), - td(["", - radio_group('ref_data', ['erc'], 'erc2', 'true', {'erc'=>' Roadmap Epigenomics (2012 data)'} )]), - td(["", - radio_group('ref_data', ['encode'], 'erc2', 'true', {'encode'=>' ENCODE'} )]), - td(["", - radio_group('ref_data', ['blueprint'], 'erc2', 'true', {'blueprint'=>' Blueprint'} )]), + popup_menu('ref_data', $ref_data_conf->{'values'}, $ref_data_conf->{'default'}, $ref_data_conf->{'labels'})]), td(["Proximity:", popup_menu('proxy', ['none', '1kb'], '1kb', {'1kb'=>'1 kb window', 'none'=>'No proxy'})]), @@ -316,8 +338,9 @@ sub validate_form { $data_format =~ s/\W/_/g; push(@error_messages, "Data format "$data_format" is not valid. Please". " specify a valid one."); + } else { + push(@$validated_args, "--format", $data_format); } - push(@$validated_args, "--format", param("data_format")); my $label = param("label"); if ($label and $label =~ /\W/) { @@ -326,20 +349,22 @@ sub validate_form { push(@$validated_args, "--label", $label) if ($label); my $bkgd = param("bkgd"); - if (!$bkgd or ($bkgd ne "450k" and $bkgd ne "27k")) { + if (!grep {$bkgd eq $_} @{$bkgd_conf->{'values'}}) { $bkgd =~ s/\W/_/g; push(@error_messages, "Unknown platform "$bkgd". Please". " specify a valid one."); + } else { + push(@$validated_args, "--bkgd", $bkgd); } - push(@$validated_args, "--bkgd", param("bkgd")); my $ref_data = param("ref_data"); - if (!$ref_data or ($ref_data ne "erc2" and $ref_data ne "erc" and $ref_data ne "encode" and $ref_data ne "blueprint")) { + if (!grep {$ref_data eq $_} @{$ref_data_conf->{'values'}}) { $ref_data =~ s/\W/_/g; push(@error_messages, "Unknown set of analysis data "$ref_data". Please". " specify a valid one."); + } else { + push(@$validated_args, "--data", $ref_data); } - push(@$validated_args, "--data", param("ref_data")); my $depletion = param("depletion"); if ($depletion and $depletion eq 'on') { From 3d1bc05a7efe9fe833615262526f062d9a5bd384 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Wed, 30 Sep 2015 11:13:24 +0100 Subject: [PATCH 08/26] Information and files to rebuild the DB from scratch --- database/README.txt | 38 ++++ database/encode.decode | 1 + database/erc.decode | 300 ++++++++++++++++++++++++++++++ database/erc2-H3-all.decode | 196 ++++++++++++++++++++ database/erc2-H3K27me3.decode | 40 ++++ database/erc2-H3K36me3.decode | 40 ++++ database/erc2-H3K4me1.decode | 40 ++++ database/erc2-H3K4me3.decode | 40 ++++ database/erc2-H3K9me3.decode | 40 ++++ database/erc2.decode | 40 ++++ database/init_db.pl | 112 ++++++++++++ database/load_450k_array.pl | 286 +++++++++++++++++++++++++++++ database/load_dataset.pl | 415 ++++++++++++++++++++++++++++++++++++++++++ 13 files changed, 1588 insertions(+) create mode 100755 database/README.txt create mode 100644 database/encode.decode create mode 100644 database/erc.decode create mode 100644 database/erc2-H3-all.decode create mode 100644 database/erc2-H3K27me3.decode create mode 100644 database/erc2-H3K36me3.decode create mode 100644 database/erc2-H3K4me1.decode create mode 100644 database/erc2-H3K4me3.decode create mode 100644 database/erc2-H3K9me3.decode create mode 100644 database/erc2.decode create mode 100644 database/init_db.pl create mode 100644 database/load_450k_array.pl create mode 100644 database/load_dataset.pl diff --git a/database/README.txt b/database/README.txt new file mode 100755 index 0000000..9c09a8b --- /dev/null +++ b/database/README.txt @@ -0,0 +1,38 @@ +This directory contains the scripts and files necessary to rebuild the eFORGE database from scratch. + +In summary, the steps are: +- Create an empty DB +- Load the information about the arrays +- Load the dataset with DHS, Histone peaks, etc +- Move the DB to its final destination + +1. CREATE AN EMPTY DATABASE + +Please refer to the help of init_db.pl for information about the different options + +rm eforge_1.1.db +perl init_db.pl --db_name eforge_1.1.db + +2. LOAD THE ARRAYS + +Please refer to the help of load_450k_array.pl for information about the different options + +perl load_450k_array.pl --work_dir input + +3. LOAD THE DATASETS + +Please refer to the help of load_dataset.pl for information about the different options + +perl load_dataset.pl --db_name eforge_1.1.db --tag erc --name 'Roadmap Epigenomics (2012 data) - DHS' --decode_file erc.decode --work_dir input/erc/ +perl load_dataset.pl --db_name eforge_1.1.db --tag encode --name 'ENCODE - DHS' --decode_file encode.decode --work_dir input/encode/ +perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-DHS --name 'Consolidated Roadmap Epigenomics - DHS' --decode_file erc2.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3K27me3 --name 'Consolidated Roadmap Epigenomics - H3K27me3' --decode_file erc2-H3K27me3.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3K36me3 --name 'Consolidated Roadmap Epigenomics - H3K36me3' --decode_file erc2-H3K36me3.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3K4me3 --name 'Consolidated Roadmap Epigenomics - H3K4me3' --decode_file erc2-H3K4me3.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3K9me3 --name 'Consolidated Roadmap Epigenomics - H3K9me3' --decode_file erc2-H3K9me3.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3K4me1 --name 'Consolidated Roadmap Epigenomics - H3K4me1' --decode_file erc2-H3K4me1.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3-all --name 'Consolidated Roadmap Epigenomics - All H3 marks' --decode_file erc2-H3-all.decode --work_dir input/erc2/ + +4. MOVE THE DATABASE TO ITS FINAL LOCATION + +mv eforge_1.1.db .. diff --git a/database/encode.decode b/database/encode.decode new file mode 100644 index 0000000..f205e22 --- /dev/null +++ b/database/encode.decode @@ -0,0 +1 @@ +file lab datatype cell tissue shortcell individual acc url A549-all.twopass.merge150.wgt10.zgt2.wig Combined DHS A549 Epithelium A549 NA "GSM816649,GSM736580,GSM736506" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/A549-all.twopass.merge150.wgt10.zgt2.wig Adult_Th0_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS Adult_CD4+ Blood Adult_CD4+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Adult_Th0_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig AG04449-DS12319.twopass.merge150.wgt10.zgt2.wig UW DHS AG04449 Skin AG04449 NA "GSM736562,GSM736590" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG04449-DS12319.twopass.merge150.wgt10.zgt2.wig AG04450-DS12270.twopass.merge150.wgt10.zgt2.wig UW DHS AG04450 Lung AG04450 NA "GSM736514,GSM736563" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG04450-DS12270.twopass.merge150.wgt10.zgt2.wig AG09309-DS12352.twopass.merge150.wgt10.zgt2.wig UW DHS AG09309 Skin AG09309 NA "GSM736551,GSM736616" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG09309-DS12352.twopass.merge150.wgt10.zgt2.wig AG09319-DS12291.twopass.merge150.wgt10.zgt2.wig UW DHS AG09319 Gingival AG09319 NA "GSM736531,GSM736619" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG09319-DS12291.twopass.merge150.wgt10.zgt2.wig AG10803-DS12384.twopass.merge150.wgt10.zgt2.wig UW DHS AG10803 Skin AG10803 NA "GSM736598,GSM736633" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG10803-DS12384.twopass.merge150.wgt10.zgt2.wig AoAF-DS13523.twopass.merge150.wgt10.zgt2.wig UW DHS AoAF Blood vessel AoAF NA "GSM736583,GSM736505" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AoAF-DS13523.twopass.merge150.wgt10.zgt2.wig BE_2_C-DS14625.twopass.merge150.wgt10.zgt2.wig UW DHS BE2_C Brain BE2_C NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/BE_2_C-DS14625.twopass.merge150.wgt10.zgt2.wig BJ-DS10081.twopass.merge150.wgt10.zgt2.wig UW DHS BJ Skin BJ NA "GSM736518,GSM736596" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/BJ-DS10081.twopass.merge150.wgt10.zgt2.wig CACO2-DS8235.twopass.merge150.wgt10.zgt2.wig UW DHS Caco-2 Colon Caco-2 NA "GSM736500,GSM736587" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CACO2-DS8235.twopass.merge150.wgt10.zgt2.wig CD14-DS18065.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS CD14+ Blood CD14+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CD14-DS18065.hg19.twopass.merge150.wgt10.zgt2.wig CD20-DS17541.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS CD20+ Blood CD20+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CD20-DS17541.hg19.twopass.merge150.wgt10.zgt2.wig CD34-DS16814.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS CD34+ Blood CD34+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CD34-DS16814.hg19.twopass.merge150.wgt10.zgt2.wig CMK-DS12393.twopass.merge150.wgt10.zgt2.wig UW DHS CMK Blood CMK NA GSM736607 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CMK-DS12393.twopass.merge150.wgt10.zgt2.wig E_myoblast_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS E_myoblast Muscle E_myoblast NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/E_myoblast_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig GM06990-DS7748.twopass.merge150.wgt10.zgt2.wig UW DHS GM06990 Blood GM06990 NA "GSM736558,GSM736635" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM06990-DS7748.twopass.merge150.wgt10.zgt2.wig GM12864-DS12431.twopass.merge150.wgt10.zgt2.wig UW DHS GM12864 Blood GM12864 NA GSM736525 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM12864-DS12431.twopass.merge150.wgt10.zgt2.wig GM12865-DS12436.twopass.merge150.wgt10.zgt2.wig UW DHS GM12865 Blood GM12865 NA "GSM736512,GSM736561" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM12865-DS12436.twopass.merge150.wgt10.zgt2.wig GM12878-all.twopass.merge150.wgt10.zgt2.wig Combined DHS GM12878 Blood GM12878 NA "GSM816665,GSM736496,GSM736620" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM12878-all.twopass.merge150.wgt10.zgt2.wig HAc-DS14765.twopass.merge150.wgt10.zgt2.wig UW DHS HAc Cerebellar HAc NA "GSM736586,GSM736538" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAc-DS14765.twopass.merge150.wgt10.zgt2.wig HAEpiC-DS12663.twopass.merge150.wgt10.zgt2.wig UW DHS HAEpiC Epithelium HAEpiC NA "GSM736631,GSM736606" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAEpiC-DS12663.twopass.merge150.wgt10.zgt2.wig HAh-DS15192.twopass.merge150.wgt10.zgt2.wig UW DHS HA-h Brain hippocampus HA-h NA "GSM736594,GSM736535" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAh-DS15192.twopass.merge150.wgt10.zgt2.wig HAsp-DS14790.twopass.merge150.wgt10.zgt2.wig UW DHS HA-sp Spinal cord HA-sp NA "GSM736537,GSM736625" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAsp-DS14790.twopass.merge150.wgt10.zgt2.wig HBMEC-DS13817.twopass.merge150.wgt10.zgt2.wig UW DHS HBMEC Blood vessel HBMEC NA "GSM736509,GSM736554" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HBMEC-DS13817.twopass.merge150.wgt10.zgt2.wig HCFaa-DS13480.twopass.merge150.wgt10.zgt2.wig UW DHS HCFaa Heart HCFaa NA "GSM736494,GSM736601" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCFaa-DS13480.twopass.merge150.wgt10.zgt2.wig HCF-DS12501.twopass.merge150.wgt10.zgt2.wig UW DHS HCF Heart HCF NA "GSM736568,GSM736540" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCF-DS12501.twopass.merge150.wgt10.zgt2.wig HCM-DS12599.twopass.merge150.wgt10.zgt2.wig UW DHS HCM Heart HCM NA "GSM736516,GSM736504" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCM-DS12599.twopass.merge150.wgt10.zgt2.wig HConF-DS11642.twopass.merge150.wgt10.zgt2.wig UW DHS HConF Eye HConF NA "GSM736547,GSM736515" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HConF-DS11642.twopass.merge150.wgt10.zgt2.wig HCPEpiC-DS12447.twopass.merge150.wgt10.zgt2.wig UW DHS HCPEpiC Epithelium HCPEpiC NA "GSM736569,GSM736597" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCPEpiC-DS12447.twopass.merge150.wgt10.zgt2.wig HCT116-DS13551.twopass.merge150.wgt10.zgt2.wig UW DHS HCT-116 Colon HCT-116 NA "GSM736600,GSM736493" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCT116-DS13551.twopass.merge150.wgt10.zgt2.wig HEEpiC-DS12763.twopass.merge150.wgt10.zgt2.wig UW DHS HEEpiC Epithelium HEEpiC NA "GSM736585,GSM736532" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HEEpiC-DS12763.twopass.merge150.wgt10.zgt2.wig Hela-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HeLa-S3 Cervix HeLa-S3 NA "GSM816633,GSM816643,GSM736564,GSM736510" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Hela-all.twopass.merge150.wgt10.zgt2.wig HepG2-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HepG2 Liver HepG2 NA "GSM816662,GSM736637,GSM736639" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HepG2-all.twopass.merge150.wgt10.zgt2.wig HESC-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HESC ES Cell HESC NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HESC-all.twopass.merge150.wgt10.zgt2.wig hESCT0-DS11909.twopass.merge150.wgt10.zgt2.wig UW DHS hESCT0 ES Cell hESCT0 NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/hESCT0-DS11909.twopass.merge150.wgt10.zgt2.wig HFF-DS15115.twopass.merge150.wgt10.zgt2.wig UW DHS HFF Foreskin HFF NA "GSM736602,GSM736572" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HFF-DS15115.twopass.merge150.wgt10.zgt2.wig HFF_MyC-DS15079.twopass.merge150.wgt10.zgt2.wig UW DHS HFF-Myc Foreskin HFF-Myc NA "GSM736524,GSM736605" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HFF_MyC-DS15079.twopass.merge150.wgt10.zgt2.wig HGF-DS11752.twopass.merge150.wgt10.zgt2.wig UW DHS HGF Gingival HGF NA "GSM736579,GSM736576" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HGF-DS11752.twopass.merge150.wgt10.zgt2.wig HIPEpiC-DS12684.twopass.merge150.wgt10.zgt2.wig UW DHS HIPEpiC Epithelium HIPEpiC NA "GSM736589,GSM736615" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HIPEpiC-DS12684.twopass.merge150.wgt10.zgt2.wig HL60-DS11809.twopass.merge150.wgt10.zgt2.wig UW DHS HL-60 Blood HL-60 NA "GSM736626,GSM736595" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HL60-DS11809.twopass.merge150.wgt10.zgt2.wig HMEC-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HMEC Breast HMEC NA "GSM816669,GSM736634,GSM736552" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMEC-all.twopass.merge150.wgt10.zgt2.wig HMF-DS13363.twopass.merge150.wgt10.zgt2.wig UW DHS HMF Breast HMF NA "GSM736628,GSM736541" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMF-DS13363.twopass.merge150.wgt10.zgt2.wig HMVEC_dAd-DS12957.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dAd Blood vessel HMVEC-dAd NA "GSM1024745,GSM1024747" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dAd-DS12957.hg19.twopass.merge150.wgt10.zgt2.wig HMVEC_dBlAd-DS13337.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dBl-Ad Blood vessel HMVEC-dBl-Ad NA "GSM736609,GSM736523" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dBlAd-DS13337.twopass.merge150.wgt10.zgt2.wig HMVEC_dBlNeo-DS13242.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dBl-Neo Blood vessel HMVEC-dBl-Neo NA "GSM736571,GSM736521" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dBlNeo-DS13242.twopass.merge150.wgt10.zgt2.wig HMVEC_dLyAd-DS13261.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dLy-Ad Blood vessel HMVEC-dLy-Ad NA "GSM736599,GSM736591" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dLyAd-DS13261.twopass.merge150.wgt10.zgt2.wig HMVEC_dLyNeo-DS13150.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dLy-Neo Blood vessel HMVEC-dLy-Neo NA "GSM736577,GSM736573" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dLyNeo-DS13150.twopass.merge150.wgt10.zgt2.wig HMVEC_dNeo-DS12937.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dNeo Blood vessel HMVEC-dNeo NA "GSM736611,GSM736624" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dNeo-DS12937.twopass.merge150.wgt10.zgt2.wig HMVEC_LBl-DS13372.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-LBl Blood vessel HMVEC-LBl NA "GSM736542,GSM736511" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_LBl-DS13372.twopass.merge150.wgt10.zgt2.wig HMVEC_LLy-DS13185.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-LLy Blood vessel HMVEC-LLy NA "GSM736507,GSM736627" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_LLy-DS13185.twopass.merge150.wgt10.zgt2.wig HNPCEpiC-DS12467.twopass.merge150.wgt10.zgt2.wig UW DHS HNPCEpiC Epithelium HNPCEpiC NA "GSM736621,GSM736550" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HNPCEpiC-DS12467.twopass.merge150.wgt10.zgt2.wig HPAEC-DS12916.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS HPAEC Blood vessel HPAEC NA GSM1024763 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPAEC-DS12916.hg19.twopass.merge150.wgt10.zgt2.wig HPAF-DS13411.twopass.merge150.wgt10.zgt2.wig UW DHS HPAF Blood vessel HPAF NA "GSM736555,GSM736614" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPAF-DS13411.twopass.merge150.wgt10.zgt2.wig HPdLF-DS13573.twopass.merge150.wgt10.zgt2.wig UW DHS HPdLF Epithelium HPdLF NA "GSM736632,GSM736528" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPdLF-DS13573.twopass.merge150.wgt10.zgt2.wig HPF-DS13390.twopass.merge150.wgt10.zgt2.wig UW DHS HPF Lung HPF NA "GSM736574,GSM736503" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPF-DS13390.twopass.merge150.wgt10.zgt2.wig HRCE-DS10666.twopass.merge150.wgt10.zgt2.wig UW DHS HRCEpiC Epithelium HRCEpiC NA "GSM736549,GSM736557" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRCE-DS10666.twopass.merge150.wgt10.zgt2.wig HRE-DS10641.twopass.merge150.wgt10.zgt2.wig UW DHS HRE Epithelium HRE NA "GSM736527,GSM736548" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRE-DS10641.twopass.merge150.wgt10.zgt2.wig HRGEC-DS13716.twopass.merge150.wgt10.zgt2.wig UW DHS HRGEC Kidney HRGEC NA "GSM736499,GSM736618" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRGEC-DS13716.twopass.merge150.wgt10.zgt2.wig HRPEpiC-DS12583.twopass.merge150.wgt10.zgt2.wig UW DHS HRPEpiC Epithelium HRPEpiC NA "GSM736630,GSM736623" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRPEpiC-DS12583.twopass.merge150.wgt10.zgt2.wig HSMM-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HSMM Muscle HSMM NA "GSM816650,GSM736560,GSM736553" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HSMM-all.twopass.merge150.wgt10.zgt2.wig HSMM_D-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HSMM Muscle HSMM NA "GSM816650,GSM736560,GSM736553" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HSMM_D-all.twopass.merge150.wgt10.zgt2.wig hTH1-all.twopass.merge150.wgt10.zgt2.wig Combined DHS Th1 Blood Th1 NA "GSM736592,GSM1024760" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/hTH1-all.twopass.merge150.wgt10.zgt2.wig hTH2-DS7842.twopass.merge150.wgt10.zgt2.wig UW DHS Th2 Blood Th2 NA "GSM736502,GSM1024792" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/hTH2-DS7842.twopass.merge150.wgt10.zgt2.wig HUVEC-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HUVEC Blood vessel HUVEC NA "GSM816646,GSM736575,GSM736533" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HUVEC-all.twopass.merge150.wgt10.zgt2.wig HVMF-DS13981.twopass.merge150.wgt10.zgt2.wig UW DHS HVMF Connective HVMF NA "GSM736534,GSM736491" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HVMF-DS13981.twopass.merge150.wgt10.zgt2.wig Ishikawa_E_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS Ishikawa Uterus Ishikawa NA "GSM1008594,GSM1008593" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Ishikawa_E_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig Ishikawa_T_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS Ishikawa Uterus Ishikawa NA "GSM1008594,GSM1008593" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Ishikawa_T_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig Jurkat-DS12659.twopass.merge150.wgt10.zgt2.wig UW DHS Jurkat Blood Jurkat NA "GSM736501,GSM736492" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Jurkat-DS12659.twopass.merge150.wgt10.zgt2.wig K562-all.twopass.merge150.wgt10.zgt2.wig Combined DHS K562 Blood K562 NA "GSM816655,GSM1008602,GSM1008567,GSM1008601,GSM1008558,GSM1008580,GSM736629,GSM736566" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/K562-all.twopass.merge150.wgt10.zgt2.wig LNCap-all.twopass.merge150.wgt10.zgt2.wig Combined DHS LNCaP Prostate LNCaP NA "GSM816637,GSM816634,GSM736565,GSM736603" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/LNCap-all.twopass.merge150.wgt10.zgt2.wig MCF7-all.twopass.merge150.wgt10.zgt2.wig Combined DHS MCF-7 Breast MCF-7 NA "GSM816627,GSM1008581,GSM816670,GSM1008565,GSM1008603,GSM1024784,GSM1024783,GSM1024764,GSM1024767,GSM736581,GSM736588" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/MCF7-all.twopass.merge150.wgt10.zgt2.wig NB4-DS12543.twopass.merge150.wgt10.zgt2.wig UW DHS NB4 Blood NB4 NA "GSM736604,GSM736529" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NB4-DS12543.twopass.merge150.wgt10.zgt2.wig NHA-DS12800.twopass.merge150.wgt10.zgt2.wig UW DHS NH-A Nervous NH-A NA "GSM736544,GSM736584" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHA-DS12800.twopass.merge150.wgt10.zgt2.wig NHDF_Ad-DS12863.twopass.merge150.wgt10.zgt2.wig UW DHS NHDF-Ad Skin NHDF-Ad NA "GSM736567,GSM736520" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHDF_Ad-DS12863.twopass.merge150.wgt10.zgt2.wig NHDF_Neo-DS11923.twopass.merge150.wgt10.zgt2.wig UW DHS NHDF-neo Skin NHDF-neo NA "GSM736498,GSM736546" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHDF_Neo-DS11923.twopass.merge150.wgt10.zgt2.wig NHEK-all.twopass.merge150.wgt10.zgt2.wig Combined DHS NHEK Skin NHEK NA "GSM816635,GSM736545,GSM736556" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHEK-all.twopass.merge150.wgt10.zgt2.wig NHLF-DS12829.twopass.merge150.wgt10.zgt2.wig UW DHS NHLF Lung NHLF NA "GSM736612,GSM736536" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHLF-DS12829.twopass.merge150.wgt10.zgt2.wig NT2_D1-DS14575.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS NT2-D1 Testis NT2-D1 NA "GSM1024751,GSM1024795" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NT2_D1-DS14575.hg19.twopass.merge150.wgt10.zgt2.wig PANC1-DS9955.twopass.merge150.wgt10.zgt2.wig UW DHS PANC-1 Pancreas PANC-1 NA "GSM736517,GSM736519" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/PANC1-DS9955.twopass.merge150.wgt10.zgt2.wig PrEC-DS12098.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS PrEC Prostate PrEC NA "GSM1024742,GSM1024743" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/PrEC-DS12098.hg19.twopass.merge150.wgt10.zgt2.wig RPTEC-DS14061.twopass.merge150.wgt10.zgt2.wig UW DHS RPTEC Epithelium RPTEC NA "GSM736543,GSM736539" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/RPTEC-DS14061.twopass.merge150.wgt10.zgt2.wig RWPE_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS RWPE1 Prostate RWPE1 NA GSM1008595 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/RWPE_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig SAEC-DS10518.twopass.merge150.wgt10.zgt2.wig UW DHS SAEC Epithelium SAEC NA "GSM736608,GSM736617" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SAEC-DS10518.twopass.merge150.wgt10.zgt2.wig SkMC-DS11949.twopass.merge150.wgt10.zgt2.wig UW DHS SKMC Muscle SKMC NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SkMC-DS11949.twopass.merge150.wgt10.zgt2.wig SK_N_MC-DS14408.twopass.merge150.wgt10.zgt2.wig UW DHS SK-N-MC Brain SK-N-MC NA "GSM736522,GSM736570" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SK_N_MC-DS14408.twopass.merge150.wgt10.zgt2.wig SKNSH-DS8482.twopass.merge150.wgt10.zgt2.wig UW DHS SK-N-SH Brain SK-N-SH NA GSM1008585 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SKNSH-DS8482.twopass.merge150.wgt10.zgt2.wig WERI_Rb1-DS13681.twopass.merge150.wgt10.zgt2.wig UW DHS WERI-Rb-1 Eye WERI-Rb-1 NA "GSM736495,GSM736636" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/WERI_Rb1-DS13681.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnase8988tAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS 8988T Liver 8988T NA GSM816667 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnase8988tAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseAosmcSerumfreeAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS AoSMC Blood vessel AoSMC NA GSM816638 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseAosmcSerumfreeAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseChorionAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Chorion Fetal membrane Chorion NA GSM816628 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseChorionAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseCllAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS CLL Blood CLL NA GSM816664 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseCllAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseFibroblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Fibrobl Skin Fibrobl NA GSM816652 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseFibroblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseFibropAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS FibroP Skin FibroP NA GSM816626 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseFibropAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseGlioblaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Gliobla Brain Gliobla NA GSM816668 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGlioblaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseGm12891AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM12891 Blood GM12891 NA GSM816656 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm12891AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseGm12892AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM12892 Blood GM12892 NA GSM816657 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm12892AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseGm18507AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM18507 Blood GM18507 NA GSM816653 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm18507AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseGm19238AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM19238 Blood GM19238 NA GSM816658 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm19238AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseGm19239AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM19239 Blood GM19239 NA GSM816659 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm19239AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseGm19240AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM19240 Blood GM19240 NA GSM816648 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm19240AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseH9esAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS H9ES ES Cell H9ES NA GSM816629 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseH9esAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseHelas3Ifna4hAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS HeLa-S3 Cervix HeLa-S3 NA "GSM816633,GSM816643,GSM736564,GSM736510" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHelas3Ifna4hAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseHepatocytesAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Hepatocytes Liver Hepatocytes NA GSM816663 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHepatocytesAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseHpde6e6e7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS HPDE6-E6E7 Pancreatic duct HPDE6-E6E7 NA GSM816639 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHpde6e6e7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseHtr8AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS HTR8svn Blastula HTR8svn NA GSM816644 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHtr8AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseHuh75AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Huh-7.5 Liver Huh-7.5 NA GSM816671 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHuh75AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseHuh7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Huh-7 Liver Huh-7 NA GSM816641 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHuh7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseIpsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS iPS IPS iPS NA GSM816642 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseIpsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseLncapAndroAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS LNCaP Prostate LNCaP NA "GSM816637,GSM816634,GSM736565,GSM736603" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseLncapAndroAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseMcf7HypoxlacAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS MCF-7 Breast MCF-7 NA "GSM816627,GSM1008581,GSM816670,GSM1008565,GSM1008603,GSM1024784,GSM1024783,GSM1024764,GSM1024767,GSM736581,GSM736588" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMcf7HypoxlacAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseMedulloAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Medullo Brain Medullo NA GSM816636 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMedulloAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseMelanoAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Melano Skin Melano NA GSM816631 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMelanoAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseMyometrAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Myometr Myometrium Myometr NA GSM816630 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMyometrAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseOsteoblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Osteobl Bone Osteobl NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseOsteoblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnasePanisdAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS PanIsletD Pancreas PanIsletD NA GSM816666 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnasePanisdAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnasePanisletsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS PanIslets Pancreas PanIslets NA GSM816660 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnasePanisletsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnasePhteAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS pHTE Epithelium pHTE NA GSM816647 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnasePhteAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseProgfibAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS ProgFib Skin ProgFib NA GSM816661 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseProgfibAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseStellateAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Stellate Liver Stellate NA GSM816672 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseStellateAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseT47dAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS T-47D Breast T-47D NA "GSM816673,GSM1008576,GSM1024762,GSM1024761" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseT47dAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseUrotsaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Urothelia Urothelium Urothelia NA "GSM1008606,GSM1008605" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseUrotsaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseUrotsaUt189AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Urothelia Urothelium Urothelia NA "GSM1008606,GSM1008605" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseUrotsaUt189AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig WI_38-DS14315.twopass.merge150.wgt10.zgt2.wig UW DHS WI-38 Embryonic lung WI-38 NA "GSM736613,GSM736526,GSM736613,GSM736526" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/WI_38-DS14315.twopass.merge150.wgt10.zgt2.wig WI_38_TAM-DS14323.twopass.merge150.wgt10.zgt2.wig UW DHS WI-38 Embryonic lung WI-38 NA "GSM736613,GSM736526,GSM736613,GSM736526" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/WI_38_TAM-DS14323.twopass.merge150.wgt10.zgt2.wig \ No newline at end of file diff --git a/database/erc.decode b/database/erc.decode new file mode 100644 index 0000000..bd80775 --- /dev/null +++ b/database/erc.decode @@ -0,0 +1,300 @@ +file lab datatype cell tissue shortcell individual acc url +UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18406.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Breast_vHMEC.RM035 Breast Breast_vHMEC RM035 GSM753973 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18406.twopass.merge150.wgt10.zgt2.wig.gz +UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18438.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Breast_vHMEC.RM035 Breast Breast_vHMEC RM035 GSM753974 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18438.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD14_Primary_Cells.ChromatinAccessibility.RO_01689.DS17391.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD14_Primary_Cells.RO_01689+ Blood CD14 RO_01689+ GSM701503 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD14_Primary_Cells.ChromatinAccessibility.RO_01689.DS17391.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD14_Primary_Cells.ChromatinAccessibility.RO_01701.DS17889.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD14_Primary_Cells.RO_01701+ Blood CD14 RO_01701+ GSM701541 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD14_Primary_Cells.ChromatinAccessibility.RO_01701.DS17889.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01679.DS17186.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD19_Primary_Cells.RO_01679+ Blood CD19 RO_01679+ GSM701492 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01679.DS17186.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01689.DS17281.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD19_Primary_Cells.RO_01689+ Blood CD19 RO_01689+ GSM701493 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01689.DS17281.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01701.DS17440.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD19_Primary_Cells.RO_01701+ Blood CD19 RO_01701+ GSM701507 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD19_Primary_Cells.ChromatinAccessibility.RO_01701.DS17440.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD20_Primary_Cells.ChromatinAccessibility.RO_01778.DS17371.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD20_Primary_Cells.RO_01778+ Blood CD20 RO_01778+ GSM701500 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD20_Primary_Cells.ChromatinAccessibility.RO_01778.DS17371.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD3_Primary_Cells.ChromatinAccessibility.CB1_1-3-2011.DS17702.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD3_Primary_Cells.CB1_1-3-2011+ Blood CD3 CB1_1-3-2011+ GSM701525 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD3_Primary_Cells.ChromatinAccessibility.CB1_1-3-2011.DS17702.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD3_Primary_Cells.ChromatinAccessibility.CB6_1-4-2011.DS17706.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD3_Primary_Cells.CB6_1-4-2011+ Blood CD3 CB6_1-4-2011+ GSM701526 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD3_Primary_Cells.ChromatinAccessibility.CB6_1-4-2011.DS17706.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD3_Primary_Cells.ChromatinAccessibility.RO_01679.DS17198.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD3_Primary_Cells.RO_01679+ Blood CD3 RO_01679+ GSM665837 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD3_Primary_Cells.ChromatinAccessibility.RO_01679.DS17198.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD3_Primary_Cells.ChromatinAccessibility.RO_01701.DS17534.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD3_Primary_Cells.RO_01701+ Blood CD3 RO_01701+ GSM701516 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD3_Primary_Cells.ChromatinAccessibility.RO_01701.DS17534.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01549.DS15947.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD4_Primary_Cells.RO_01549+ Blood CD4 RO_01549+ GSM665812 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01549.DS15947.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01679.DS17212.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD4_Primary_Cells.RO_01679+ Blood CD4 RO_01679+ GSM665839 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01679.DS17212.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01689.DS17329.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD4_Primary_Cells.RO_01689+ Blood CD4 RO_01689+ GSM817166 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01689.DS17329.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01701.DS17881.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD4_Primary_Cells.RO_01701+ Blood CD4 RO_01701+ GSM701539 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD4_Primary_Cells.ChromatinAccessibility.RO_01701.DS17881.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD56_Primary_Cells.ChromatinAccessibility.RO_01679.DS17189.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD56_Primary_Cells.RO_01679+ Blood CD56 RO_01679+ GSM665836 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD56_Primary_Cells.ChromatinAccessibility.RO_01679.DS17189.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD56_Primary_Cells.ChromatinAccessibility.RO_01701.DS17443.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD56_Primary_Cells.RO_01701+ Blood CD56 RO_01701+ GSM701508 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD56_Primary_Cells.ChromatinAccessibility.RO_01701.DS17443.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01549.DS16012.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD8_Primary_Cells.RO_01549+ Blood CD8 RO_01549+ GSM665813 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01549.DS16012.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01679.DS17203.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD8_Primary_Cells.RO_01679+ Blood CD8 RO_01679+ GSM665838 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01679.DS17203.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01689.DS17332.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD8_Primary_Cells.RO_01689+ Blood CD8 RO_01689+ GSM701499 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01689.DS17332.twopass.merge150.wgt10.zgt2.wig.gz +UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01701.DS17885.twopass.merge150.wgt10.zgt2.wig.gz UW DHS CD8_Primary_Cells.RO_01701+ Blood CD8 RO_01701+ GSM701540 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.CD8_Primary_Cells.ChromatinAccessibility.RO_01701.DS17885.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-22662.DS12528.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Adrenal_Gland.H-22662 Fetal Adrenal Fetal_Adrenal_Gland H-22662 GSM530653 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-22662.DS12528.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-23769.DS17319.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Adrenal_Gland.H-23769 Fetal Adrenal Fetal_Adrenal_Gland H-23769 GSM817165 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-23769.DS17319.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-24409.DS20343.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Adrenal_Gland.H-24409 Fetal Adrenal Fetal_Adrenal_Gland H-24409 GSM878658 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-24409.DS20343.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-22510.DS11872.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-22510 Fetal Brain Fetal_Brain H-22510 GSM530651 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-22510.DS11872.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-22510.DS11877.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-22510 Fetal Brain Fetal_Brain H-22510 GSM595913 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-22510.DS11877.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-22911.DS14464.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-22911 Fetal Brain Fetal_Brain H-22911 GSM595920 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-22911.DS14464.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14717.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-23266 Fetal Brain Fetal_Brain H-23266 GSM595922 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14717.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14718.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-23266 Fetal Brain Fetal_Brain H-23266 GSM595923 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14718.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-23284.DS14803.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-23284 Fetal Brain Fetal_Brain H-23284 GSM595926 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-23284.DS14803.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-23284.DS14815.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-23284 Fetal Brain Fetal_Brain H-23284 GSM595928 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-23284.DS14815.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-23399.DS15453.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-23399 Fetal Brain Fetal_Brain H-23399 GSM665804 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-23399.DS15453.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-23548.DS16302.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-23548 Fetal Brain Fetal_Brain H-23548 GSM665819 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-23548.DS16302.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-24279.DS20221.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-24279 Fetal Brain Fetal_Brain H-24279 GSM878650 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-24279.DS20221.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-24297.DS20226.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-24297 Fetal Brain Fetal_Brain H-24297 GSM878651 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-24297.DS20226.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Brain.ChromatinAccessibility.H-24381.DS20231.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Brain.H-24381 Fetal Brain Fetal_Brain H-24381 GSM878652 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Brain.ChromatinAccessibility.H-24381.DS20231.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-22662.DS12531.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-22662 Fetal Heart Fetal_Heart H-22662 GSM530654 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-22662.DS12531.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-22727.DS12810.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-22727 Fetal Heart Fetal_Heart H-22727 GSM530661 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-22727.DS12810.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-23468.DS15839.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-23468 Fetal Heart Fetal_Heart H-23468 GSM665811 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-23468.DS15839.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-23500.DS16018.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-23500 Fetal Heart Fetal_Heart H-23500 GSM665814 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-23500.DS16018.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-23524.DS16146.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-23524 Fetal Heart Fetal_Heart H-23524 GSM665817 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-23524.DS16146.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-23589.DS16500.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-23589 Fetal Heart Fetal_Heart H-23589 GSM665824 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-23589.DS16500.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-23604.DS16582.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-23604 Fetal Heart Fetal_Heart H-23604 GSM665830 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-23604.DS16582.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-23617.DS16621.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-23617 Fetal Heart Fetal_Heart H-23617 GSM665831 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-23617.DS16621.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-23663.DS16819.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-23663 Fetal Heart Fetal_Heart H-23663 GSM774203 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-23663.DS16819.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-23744.DS19431.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-23744 Fetal Heart Fetal_Heart H-23744 GSM817220 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-23744.DS19431.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Heart.ChromatinAccessibility.H-24042.DS19427.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Heart.H-24042 Fetal Heart Fetal_Heart H-24042 GSM878630 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Heart.ChromatinAccessibility.H-24042.DS19427.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23500.DS16027.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23500 "Fetal Intestine, Large" Fetal_Intestine_Large H-23500 GSM665815 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23500.DS16027.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23524.DS16164.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23524 "Fetal Intestine, Large" Fetal_Intestine_Large H-23524 GSM665818 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23524.DS16164.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23604.DS16563.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23604 "Fetal Intestine, Large" Fetal_Intestine_Large H-23604 GSM665826 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23604.DS16563.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23744.DS17094.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23744 "Fetal Intestine, Large" Fetal_Intestine_Large H-23744 GSM817162 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23744.DS17094.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23758.DS17157.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23758 "Fetal Intestine, Large" Fetal_Intestine_Large H-23758 GSM701490 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23758.DS17157.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23769.DS17313.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23769 "Fetal Intestine, Large" Fetal_Intestine_Large H-23769 GSM701495 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23769.DS17313.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23808.DS17422.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23808 "Fetal Intestine, Large" Fetal_Intestine_Large H-23808 GSM774213 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23808.DS17422.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23833.DS17462.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23833 "Fetal Intestine, Large" Fetal_Intestine_Large H-23833 GSM774214 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23833.DS17462.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23855.DS17502.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23855 "Fetal Intestine, Large" Fetal_Intestine_Large H-23855 GSM701514 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23855.DS17502.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23887.DS17647.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23887 "Fetal Intestine, Large" Fetal_Intestine_Large H-23887 GSM774217 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23887.DS17647.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23914.DS17748.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23914 "Fetal Intestine, Large" Fetal_Intestine_Large H-23914 GSM774220 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23914.DS17748.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23941.DS17785.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23941 "Fetal Intestine, Large" Fetal_Intestine_Large H-23941 GSM701531 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23941.DS17785.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23964.DS17841.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-23964 "Fetal Intestine, Large" Fetal_Intestine_Large H-23964 GSM774228 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-23964.DS17841.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-24005.DS17990.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-24005 "Fetal Intestine, Large" Fetal_Intestine_Large H-24005 GSM774233 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-24005.DS17990.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Large.ChromatinAccessibility.H-24111.DS18499.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Large.H-24111 "Fetal Intestine, Large" Fetal_Intestine_Large H-24111 GSM817188 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Large.ChromatinAccessibility.H-24111.DS18499.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23604.DS16559.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23604 "Fetal Intestine, Small" Fetal_Intestine_Small H-23604 GSM665825 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23604.DS16559.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23640.DS16712.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23640 "Fetal Intestine, Small" Fetal_Intestine_Small H-23640 GSM701487 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23640.DS16712.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23663.DS16822.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23663 "Fetal Intestine, Small" Fetal_Intestine_Small H-23663 GSM665835 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23663.DS16822.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23724.DS16975.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23724 "Fetal Intestine, Small" Fetal_Intestine_Small H-23724 GSM817161 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23724.DS16975.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23744.DS17092.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23744 "Fetal Intestine, Small" Fetal_Intestine_Small H-23744 GSM774205 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23744.DS17092.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23758.DS17150.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23758 "Fetal Intestine, Small" Fetal_Intestine_Small H-23758 GSM774210 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23758.DS17150.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23769.DS17317.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23769 "Fetal Intestine, Small" Fetal_Intestine_Small H-23769 GSM701496 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23769.DS17317.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23808.DS17425.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23808 "Fetal Intestine, Small" Fetal_Intestine_Small H-23808 GSM701504 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23808.DS17425.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23864.DS17844.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23864 "Fetal Intestine, Small" Fetal_Intestine_Small H-23864 GSM774229 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23864.DS17844.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23887.DS17643.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23887 "Fetal Intestine, Small" Fetal_Intestine_Small H-23887 GSM774216 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23887.DS17643.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23914.DS17763.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23914 "Fetal Intestine, Small" Fetal_Intestine_Small H-23914 GSM701530 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23914.DS17763.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23941.DS17808.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-23941 "Fetal Intestine, Small" Fetal_Intestine_Small H-23941 GSM774225 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-23941.DS17808.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Intestine_Small.ChromatinAccessibility.H-24111.DS18495.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Intestine_Small.H-24111 "Fetal Intestine, Small" Fetal_Intestine_Small H-24111 GSM817187 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Intestine_Small.ChromatinAccessibility.H-24111.DS18495.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney.ChromatinAccessibility.H-22337.DS10986.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney.H-22337 Fetal Kidney Fetal_Kidney H-22337 GSM493385 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney.ChromatinAccessibility.H-22337.DS10986.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney.ChromatinAccessibility.H-22676.DS12635.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney.H-22676 Fetal Kidney Fetal_Kidney H-22676 GSM530655 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney.ChromatinAccessibility.H-22676.DS12635.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney.ChromatinAccessibility.H-23524.DS16139.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney.H-23524 Fetal Kidney Fetal_Kidney H-23524 GSM665816 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney.ChromatinAccessibility.H-23524.DS16139.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney.ChromatinAccessibility.H-23663.DS16837.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney.H-23663 Fetal Kidney Fetal_Kidney H-23663 GSM817159 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney.ChromatinAccessibility.H-23663.DS16837.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney.ChromatinAccessibility.H-23855.DS17522.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney.H-23855 Fetal Kidney Fetal_Kidney H-23855 GSM701515 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney.ChromatinAccessibility.H-23855.DS17522.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney.ChromatinAccessibility.H-23914.DS17753.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney.H-23914 Fetal Kidney Fetal_Kidney H-23914 GSM774221 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney.ChromatinAccessibility.H-23914.DS17753.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney.ChromatinAccessibility.H-24507.DS20564.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney.H-24507 Fetal Kidney Fetal_Kidney H-24507 GSM878666 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney.ChromatinAccessibility.H-24507.DS20564.twopass.merge150.wgt10.zgt2.wig.gz 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ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23640.DS16805.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23758.DS17140.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney_Left.H-23758 Fetal Kidney Fetal_Kidney_Left H-23758 GSM774209 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23758.DS17140.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24089.DS18466.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney_Left.H-24089 Fetal Kidney Fetal_Kidney_Left H-24089 GSM817181 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24089.DS18466.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Kidney_Right.ChromatinAccessibility.H-23435.DS15651.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Kidney_Right.H-23435 Fetal Kidney Fetal_Kidney_Right H-23435 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ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Right.ChromatinAccessibility.H-23758.DS17162.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Right.ChromatinAccessibility.H-23887.DS17670.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Right.H-23887 Fetal Lung Fetal_Lung_Right H-23887 GSM701523 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Right.ChromatinAccessibility.H-23887.DS17670.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Right.ChromatinAccessibility.H-23964.DS17831.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Right.H-23964 Fetal Lung Fetal_Lung_Right H-23964 GSM774227 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Right.ChromatinAccessibility.H-23964.DS17831.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Right.ChromatinAccessibility.H-24005.DS17954.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Right.H-24005 Fetal Lung Fetal_Lung_Right H-24005 GSM774231 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Right.ChromatinAccessibility.H-24005.DS17954.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Right.ChromatinAccessibility.H-24089.DS18418.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Right.H-24089 Fetal Lung Fetal_Lung_Right H-24089 GSM817174 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Right.ChromatinAccessibility.H-24089.DS18418.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Lung_Right.ChromatinAccessibility.H-24111.DS18492.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Lung_Right.H-24111 Fetal Lung Fetal_Lung_Right H-24111 GSM817186 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Lung_Right.ChromatinAccessibility.H-24111.DS18492.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23808.DS17432.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-23808 Fetal Muscle Fetal_Muscle_Arm H-23808 GSM701506 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23808.DS17432.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23914.DS17765.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-23914 Fetal Muscle Fetal_Muscle_Arm H-23914 GSM774223 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23914.DS17765.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23941.DS17825.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-23941 Fetal Muscle Fetal_Muscle_Arm H-23941 GSM774226 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23941.DS17825.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23964.DS17848.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-23964 Fetal Muscle Fetal_Muscle_Arm H-23964 GSM701535 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-23964.DS17848.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24005.DS18080.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24005 Fetal Muscle Fetal_Muscle_Arm H-24005 GSM774234 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24005.DS18080.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24042.DS18176.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24042 Fetal Muscle Fetal_Muscle_Arm H-24042 GSM774239 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24042.DS18176.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24078.DS18379.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24078 Fetal Muscle Fetal_Muscle_Arm H-24078 GSM878610 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24078.DS18379.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24089.DS18452.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24089 Fetal Muscle Fetal_Muscle_Arm H-24089 GSM817178 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24089.DS18452.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24111.DS18473.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24111 Fetal Muscle Fetal_Muscle_Arm H-24111 GSM817184 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24111.DS18473.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24125.DS18559.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24125 Fetal Muscle Fetal_Muscle_Arm H-24125 GSM817191 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ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24272.DS19380.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24297.DS19646.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Arm.H-24297 Fetal Muscle Fetal_Muscle_Arm H-24297 GSM878638 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24297.DS19646.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-23914.DS17767.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-23914 Fetal Muscle Fetal_Muscle_Back H-23914 GSM774224 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-23914.DS17767.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-23964.DS17850.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-23964 Fetal Muscle Fetal_Muscle_Back H-23964 GSM701536 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-23964.DS17850.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24005.DS18083.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24005 Fetal Muscle Fetal_Muscle_Back H-24005 GSM774235 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24005.DS18083.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24078.DS18377.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24078 Fetal Muscle Fetal_Muscle_Back H-24078 GSM817171 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24078.DS18377.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24089.DS18454.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24089 Fetal Muscle Fetal_Muscle_Back H-24089 GSM878611 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24089.DS18454.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24111.DS18468.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24111 Fetal Muscle Fetal_Muscle_Back H-24111 GSM817182 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24111.DS18468.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24143.DS18842.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24143 Fetal Muscle Fetal_Muscle_Back H-24143 GSM817200 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24143.DS18842.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24218.DS19117.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24218 Fetal Muscle Fetal_Muscle_Back H-24218 GSM817207 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24218.DS19117.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24244.DS19283.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24244 Fetal Muscle Fetal_Muscle_Back H-24244 GSM817212 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24244.DS19283.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24272.DS19384.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24272 Fetal Muscle Fetal_Muscle_Back H-24272 GSM817217 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24272.DS19384.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24279.DS19441.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24279 Fetal Muscle Fetal_Muscle_Back H-24279 GSM878632 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24279.DS19441.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24297.DS19648.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24297 Fetal Muscle Fetal_Muscle_Back H-24297 GSM878639 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24297.DS19648.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24409.DS20244.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Back.H-24409 Fetal Muscle Fetal_Muscle_Back H-24409 GSM878655 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24409.DS20244.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-23808.DS17429.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-23808 Fetal Muscle Fetal_Muscle_Leg H-23808 GSM701505 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-23808.DS17429.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24078.DS18386.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24078 Fetal Muscle Fetal_Muscle_Leg H-24078 GSM774242 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24078.DS18386.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24089.DS18456.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24089 Fetal Muscle Fetal_Muscle_Leg H-24089 GSM817179 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24089.DS18456.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24111.DS18471.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24111 Fetal Muscle Fetal_Muscle_Leg H-24111 GSM817183 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24111.DS18471.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24143.DS18844.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24143 Fetal Muscle Fetal_Muscle_Leg H-24143 GSM817201 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24143.DS18844.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24198.DS19158.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24198 Fetal Muscle Fetal_Muscle_Leg H-24198 GSM878622 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24198.DS19158.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24218.DS19115.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24218 Fetal Muscle Fetal_Muscle_Leg H-24218 GSM817206 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24218.DS19115.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24244.DS19272.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24244 Fetal Muscle Fetal_Muscle_Leg H-24244 GSM878626 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24244.DS19272.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24259.DS19291.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24259 Fetal Muscle Fetal_Muscle_Leg H-24259 GSM817213 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24259.DS19291.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24279.DS19436.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24279 Fetal Muscle Fetal_Muscle_Leg H-24279 GSM878631 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24279.DS19436.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24297.DS19643.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24297 Fetal Muscle Fetal_Muscle_Leg H-24297 GSM878637 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24297.DS19643.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24409.DS20239.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Leg.H-24409 Fetal Muscle Fetal_Muscle_Leg H-24409 GSM878653 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24409.DS20239.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Lower_Limb_Skeletal.ChromatinAccessibility.H-24042.DS18174.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Lower_Limb_Skeletal.H-24042 Fetal Muscle Fetal_Muscle_Lower_Limb_Skeletal H-24042 GSM774238 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Lower_Limb_Skeletal.ChromatinAccessibility.H-24042.DS18174.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Trunk.ChromatinAccessibility.H-23941.DS17827.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Trunk.H-23941 Fetal Muscle Fetal_Muscle_Trunk H-23941 GSM701533 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Trunk.ChromatinAccessibility.H-23941.DS17827.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Trunk.ChromatinAccessibility.H-24409.DS20242.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Trunk.H-24409 Fetal Muscle Fetal_Muscle_Trunk H-24409 GSM878654 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Trunk.ChromatinAccessibility.H-24409.DS20242.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Trunk.ChromatinAccessibility.H-24507.DS20544.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Trunk.H-24507 Fetal Muscle Fetal_Muscle_Trunk H-24507 GSM878664 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Trunk.ChromatinAccessibility.H-24507.DS20544.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Upper_Limb_Skeletal.ChromatinAccessibility.H-23887.DS17661.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Upper_Limb_Skeletal.H-23887 Fetal Muscle Fetal_Muscle_Upper_Limb_Skeletal H-23887 GSM701522 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Upper_Limb_Skeletal.ChromatinAccessibility.H-23887.DS17661.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Muscle_Upper_Trunk.ChromatinAccessibility.H-23887.DS17664.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Muscle_Upper_Trunk.H-23887 Fetal Muscle Fetal_Muscle_Upper_Trunk H-23887 GSM774218 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Muscle_Upper_Trunk.ChromatinAccessibility.H-23887.DS17664.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Placenta.ChromatinAccessibility.H-23887.DS17639.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Placenta.H-23887 Fetal Placenta Fetal_Placenta H-23887 GSM774215 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Placenta.ChromatinAccessibility.H-23887.DS17639.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Placenta.ChromatinAccessibility.H-23914.DS17744.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Placenta.H-23914 Fetal Placenta Fetal_Placenta H-23914 GSM774219 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Placenta.ChromatinAccessibility.H-23914.DS17744.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Placenta.ChromatinAccessibility.H-24272.DS19391.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Placenta.H-24272 Fetal Placenta Fetal_Placenta H-24272 GSM817219 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Placenta.ChromatinAccessibility.H-24272.DS19391.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Placenta.ChromatinAccessibility.H-24409.DS20346.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Placenta.H-24409 Fetal Placenta Fetal_Placenta H-24409 GSM878659 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Placenta.ChromatinAccessibility.H-24409.DS20346.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23769.DS17307.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex.H-23769 Fetal Renal Cortex Fetal_Renal_Cortex H-23769 GSM701494 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23769.DS17307.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23790.DS17387.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex.H-23790 Fetal Renal Cortex Fetal_Renal_Cortex H-23790 GSM701502 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23790.DS17387.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23833.DS17455.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex.H-23833 Fetal Renal Cortex Fetal_Renal_Cortex H-23833 GSM701511 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23833.DS17455.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23914.DS17756.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex.H-23914 Fetal Renal Cortex Fetal_Renal_Cortex H-23914 GSM701529 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23914.DS17756.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23941.DS17804.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex.H-23941 Fetal Renal Cortex Fetal_Renal_Cortex H-23941 GSM701532 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-23941.DS17804.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24078.DS18428.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex.H-24078 Fetal Renal Cortex Fetal_Renal_Cortex H-24078 GSM817176 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24078.DS18428.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24259.DS19388.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex.H-24259 Fetal Renal Cortex Fetal_Renal_Cortex H-24259 GSM878629 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24259.DS19388.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24493.DS20568.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex.H-24493 Fetal Renal Cortex Fetal_Renal_Cortex H-24493 GSM878667 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24493.DS20568.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-23871.DS17550.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex_Left.H-23871 Fetal Renal Cortex Fetal_Renal_Cortex_Left H-23871 GSM701519 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-23871.DS17550.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24111.DS18542.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex_Left.H-24111 Fetal Renal Cortex Fetal_Renal_Cortex_Left H-24111 GSM817190 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24111.DS18542.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24169.DS18931.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex_Left.H-24169 Fetal Renal Cortex Fetal_Renal_Cortex_Left H-24169 GSM817203 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24169.DS18931.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24232.DS19257.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex_Left.H-24232 Fetal Renal Cortex Fetal_Renal_Cortex_Left H-24232 GSM817211 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24232.DS19257.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-23871.DS17545.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex_Right.H-23871 Fetal Renal Cortex Fetal_Renal_Cortex_Right H-23871 GSM701517 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-23871.DS17545.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-24169.DS18928.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex_Right.H-24169 Fetal Renal Cortex Fetal_Renal_Cortex_Right H-24169 GSM817202 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-24169.DS18928.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-24232.DS19254.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Cortex_Right.H-24232 Fetal Renal Cortex Fetal_Renal_Cortex_Right H-24232 GSM817210 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-24232.DS19254.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23790.DS17381.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis.H-23790 Fetal Renal Pelvis Fetal_Renal_Pelvis H-23790 GSM701501 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23790.DS17381.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23833.DS17451.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis.H-23833 Fetal Renal Pelvis Fetal_Renal_Pelvis H-23833 GSM701510 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23833.DS17451.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23914.DS17760.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis.H-23914 Fetal Renal Pelvis Fetal_Renal_Pelvis H-23914 GSM774222 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-23914.DS17760.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24005.DS18088.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis.H-24005 Fetal Renal Pelvis Fetal_Renal_Pelvis H-24005 GSM774236 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24005.DS18088.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24078.DS18431.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis.H-24078 Fetal Renal Pelvis Fetal_Renal_Pelvis H-24078 GSM817177 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24078.DS18431.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24259.DS19386.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis.H-24259 Fetal Renal Pelvis Fetal_Renal_Pelvis H-24259 GSM817218 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24259.DS19386.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24477.DS20448.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis.H-24477 Fetal Renal Pelvis Fetal_Renal_Pelvis H-24477 GSM878662 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24477.DS20448.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-23871.DS17553.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis_Left.H-23871 Fetal Renal Pelvis Fetal_Renal_Pelvis_Left H-23871 GSM701520 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-23871.DS17553.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24111.DS18666.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis_Left.H-24111 Fetal Renal Pelvis Fetal_Renal_Pelvis_Left H-24111 GSM817193 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24111.DS18666.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24169.DS18964.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis_Left.H-24169 Fetal Renal Pelvis Fetal_Renal_Pelvis_Left H-24169 GSM817205 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24169.DS18964.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24232.DS19238.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis_Left.H-24232 Fetal Renal Pelvis Fetal_Renal_Pelvis_Left H-24232 GSM817209 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24232.DS19238.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-23871.DS17548.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis_Right.H-23871 Fetal Renal Pelvis Fetal_Renal_Pelvis_Right H-23871 GSM701518 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-23871.DS17548.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24111.DS18663.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis_Right.H-24111 Fetal Renal Pelvis Fetal_Renal_Pelvis_Right H-24111 GSM817192 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24111.DS18663.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24169.DS18961.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis_Right.H-24169 Fetal Renal Pelvis Fetal_Renal_Pelvis_Right H-24169 GSM817204 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24169.DS18961.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24232.DS19235.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Renal_Pelvis_Right.H-24232 Fetal Renal Pelvis Fetal_Renal_Pelvis_Right H-24232 GSM817208 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24232.DS19235.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Skin.ChromatinAccessibility.H-22337.DS10987.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Skin.H-22337 Fetal Skin Fetal_Skin H-22337 GSM817158 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Skin.ChromatinAccessibility.H-22337.DS10987.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24111.DS18501.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Spinal_Cord.H-24111 Fetal Spinal Cord Fetal_Spinal_Cord H-24111 GSM817189 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24111.DS18501.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24409.DS20351.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Spinal_Cord.H-24409 Fetal Spinal Cord Fetal_Spinal_Cord H-24409 GSM878661 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24409.DS20351.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24493.DS20530.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Spinal_Cord.H-24493 Fetal Spinal Cord Fetal_Spinal_Cord H-24493 GSM878663 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24493.DS20530.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Spleen.ChromatinAccessibility.H-23399.DS17448.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Spleen.H-23399 Fetal Spleen Fetal_Spleen H-23399 GSM701509 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Spleen.ChromatinAccessibility.H-23399.DS17448.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-23589.DS16530.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-23589 Fetal Stomach Fetal_Stomach H-23589 GSM774202 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-23589.DS16530.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-23758.DS17172.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-23758 Fetal Stomach Fetal_Stomach H-23758 GSM774212 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-23758.DS17172.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-23769.DS17325.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-23769 Fetal Stomach Fetal_Stomach H-23769 GSM701498 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-23769.DS17325.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-23887.DS17659.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-23887 Fetal Stomach Fetal_Stomach H-23887 GSM701521 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-23887.DS17659.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-23914.DS17750.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-23914 Fetal Stomach Fetal_Stomach H-23914 GSM701528 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-23914.DS17750.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-23964.DS17878.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-23964 Fetal Stomach Fetal_Stomach H-23964 GSM701538 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-23964.DS17878.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-24005.DS17963.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-24005 Fetal Stomach Fetal_Stomach H-24005 GSM774232 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-24005.DS17963.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-24078.DS18389.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-24078 Fetal Stomach Fetal_Stomach H-24078 GSM817173 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-24078.DS18389.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-24125.DS18821.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-24125 Fetal Stomach Fetal_Stomach H-24125 GSM817199 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-24125.DS18821.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-24401.DS20349.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-24401 Fetal Stomach Fetal_Stomach H-24401 GSM878660 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-24401.DS20349.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Stomach.ChromatinAccessibility.H-24507.DS20546.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Stomach.H-24507 Fetal Stomach Fetal_Stomach H-24507 GSM878665 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Stomach.ChromatinAccessibility.H-24507.DS20546.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Testes.ChromatinAccessibility.H24198_H23640_H24042.DS18942.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Testes.H24198_H23640_H24042 Fetal Testes Fetal_Testes H24198_H23640_H24042 GSM878617 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Testes.ChromatinAccessibility.H24198_H23640_H24042.DS18942.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-23589.DS16490.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-23589 Fetal Thymus Fetal_Thymus H-23589 GSM665823 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-23589.DS16490.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-23663.DS16841.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-23663 Fetal Thymus Fetal_Thymus H-23663 GSM774204 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-23663.DS16841.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-23769.DS17323.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-23769 Fetal Thymus Fetal_Thymus H-23769 GSM701497 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-23769.DS17323.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-23833.DS17474.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-23833 Fetal Thymus Fetal_Thymus H-23833 GSM701513 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-23833.DS17474.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17875.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-23964 Fetal Thymus Fetal_Thymus H-23964 GSM701537 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17875.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17876.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-23964 Fetal Thymus Fetal_Thymus H-23964 GSM774230 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-23964.DS17876.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-24078.DS18382.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-24078 Fetal Thymus Fetal_Thymus H-24078 GSM817172 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-24078.DS18382.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-24259.DS19287.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-24259 Fetal Thymus Fetal_Thymus H-24259 GSM878627 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-24259.DS19287.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-24401.DS20335.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-24401 Fetal Thymus Fetal_Thymus H-24401 GSM878656 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-24401.DS20335.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fetal_Thymus.ChromatinAccessibility.H-24409.DS20341.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fetal_Thymus.H-24409 Fetal Thymus Fetal_Thymus H-24409 GSM878657 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fetal_Thymus.ChromatinAccessibility.H-24409.DS20341.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Abdomen.ChromatinAccessibility.H-24259.DS19558.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Abdomen.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Abdomen H-24259 GSM878635 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Abdomen.ChromatinAccessibility.H-24259.DS19558.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Abdomen.ChromatinAccessibility.H-24259.DS19561.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Abdomen.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Abdomen H-24259 GSM878636 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Abdomen.ChromatinAccessibility.H-24259.DS19561.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Back.ChromatinAccessibility.H-24218.DS19233.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Back.H-24218 Fibroblast Fibroblasts_Fetal_Skin_Back H-24218 GSM878624 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Back.ChromatinAccessibility.H-24218.DS19233.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Biceps_Left.ChromatinAccessibility.H-24259.DS19857.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Biceps_Left.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Biceps_Left H-24259 GSM878644 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Biceps_Left.ChromatinAccessibility.H-24259.DS19857.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Biceps_Left.ChromatinAccessibility.H-24259.DS19867.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Biceps_Left.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Biceps_Left H-24259 GSM878645 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Biceps_Left.ChromatinAccessibility.H-24259.DS19867.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Biceps_Right.ChromatinAccessibility.H-24259.DS19745.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Biceps_Right.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Biceps_Right H-24259 GSM878642 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Biceps_Right.ChromatinAccessibility.H-24259.DS19745.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Biceps_Right.ChromatinAccessibility.H-24259.DS19761.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Biceps_Right.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Biceps_Right H-24259 GSM878643 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Biceps_Right.ChromatinAccessibility.H-24259.DS19761.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Quadriceps_Left.ChromatinAccessibility.H-24259.DS20046.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Quadriceps_Left.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Quadriceps_Left H-24259 GSM878648 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Quadriceps_Left.ChromatinAccessibility.H-24259.DS20046.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Quadriceps_Left.ChromatinAccessibility.H-24259.DS20056.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Quadriceps_Left.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Quadriceps_Left H-24259 GSM878649 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Quadriceps_Left.ChromatinAccessibility.H-24259.DS20056.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Quadriceps_Right.ChromatinAccessibility.H-24259.DS19943.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Quadriceps_Right.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Quadriceps_Right H-24259 GSM878646 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Quadriceps_Right.ChromatinAccessibility.H-24259.DS19943.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Quadriceps_Right.ChromatinAccessibility.H-24259.DS19948.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Quadriceps_Right.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Quadriceps_Right H-24259 GSM878647 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Quadriceps_Right.ChromatinAccessibility.H-24259.DS19948.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Scalp.ChromatinAccessibility.H-24259.DS19444.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Scalp.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Scalp H-24259 GSM878633 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Scalp.ChromatinAccessibility.H-24259.DS19444.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Scalp.ChromatinAccessibility.H-24259.DS19449.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Scalp.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Scalp H-24259 GSM878634 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Scalp.ChromatinAccessibility.H-24259.DS19449.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Upper_Back.ChromatinAccessibility.H-24259.DS19696.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Upper_Back.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Upper_Back H-24259 GSM878640 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Upper_Back.ChromatinAccessibility.H-24259.DS19696.twopass.merge150.wgt10.zgt2.wig.gz +UW.Fibroblasts_Fetal_Skin_Upper_Back.ChromatinAccessibility.H-24259.DS19706.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Fibroblasts_Fetal_Skin_Upper_Back.H-24259 Fibroblast Fibroblasts_Fetal_Skin_Upper_Back H-24259 GSM878641 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Fibroblasts_Fetal_Skin_Upper_Back.ChromatinAccessibility.H-24259.DS19706.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS18732.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1_BMP4_Derived_Mesendoderm_Cultured_Cells ES Cell Mesendoderm_Cultured_Cells NA GSM817198 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS18732.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS19310.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1_BMP4_Derived_Mesendoderm_Cultured_Cells ES Cell Mesendoderm_Cultured_Cells NA GSM817215 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS19310.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1_BMP4_Derived_Trophoblast_Cultured_Cells.ChromatinAccessibility.DS18736.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1_BMP4_Derived_Trophoblast_Cultured_Cells ES Cell Trophoblast_Cultured_Cells NA GSM878614 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1_BMP4_Derived_Trophoblast_Cultured_Cells.ChromatinAccessibility.DS18736.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1_BMP4_Derived_Trophoblast_Cultured_Cells.ChromatinAccessibility.DS19317.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1_BMP4_Derived_Trophoblast_Cultured_Cells ES Cell Trophoblast_Cultured_Cells NA GSM878628 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1_BMP4_Derived_Trophoblast_Cultured_Cells.ChromatinAccessibility.DS19317.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1.ChromatinAccessibility.DS18873.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1 ES Cell H1 NA GSM878616 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1.ChromatinAccessibility.DS18873.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1.ChromatinAccessibility.DS19100.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1 ES Cell H1 NA GSM878621 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1.ChromatinAccessibility.DS19100.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1_Derived_Mesenchymal_Stem_Cells.ChromatinAccessibility.DS20671.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1_Derived_Mesenchymal_Stem_Cells ES Cell Mesenchymal_Stem_Cells NA GSM906380 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1_Derived_Mesenchymal_Stem_Cells.ChromatinAccessibility.DS20671.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1_Derived_Mesenchymal_Stem_Cells.ChromatinAccessibility.DS21042.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1_Derived_Mesenchymal_Stem_Cells ES Cell Mesenchymal_Stem_Cells NA GSM906381 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1_Derived_Mesenchymal_Stem_Cells.ChromatinAccessibility.DS21042.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1_Derived_Neuronal_Progenitor_Cultured_Cells.ChromatinAccessibility.DS18739.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1_Derived_Neuronal_Progenitor_Cultured_Cells ES Cell Neuronal_Progenitor_Cultured_Cells NA GSM878615 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1_Derived_Neuronal_Progenitor_Cultured_Cells.ChromatinAccessibility.DS18739.twopass.merge150.wgt10.zgt2.wig.gz +UW.H1_Derived_Neuronal_Progenitor_Cultured_Cells.ChromatinAccessibility.DS20153.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H1_Derived_Neuronal_Progenitor_Cultured_Cells ES Cell Neuronal_Progenitor_Cultured_Cells NA GSM906379 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H1_Derived_Neuronal_Progenitor_Cultured_Cells.ChromatinAccessibility.DS20153.twopass.merge150.wgt10.zgt2.wig.gz +UW.H9.ChromatinAccessibility.DS18517.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H9 ES Cell H9 NA GSM878612 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H9.ChromatinAccessibility.DS18517.twopass.merge150.wgt10.zgt2.wig.gz +UW.H9.ChromatinAccessibility.DS18522.twopass.merge150.wgt10.zgt2.wig.gz UW DHS H9 ES Cell H9 NA GSM878613 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.H9.ChromatinAccessibility.DS18522.twopass.merge150.wgt10.zgt2.wig.gz +UW.IMR90.ChromatinAccessibility.DS11759.twopass.merge150.wgt10.zgt2.wig.gz UW DHS IMR90 Lung IMR90 NA GSM468792 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.IMR90.ChromatinAccessibility.DS11759.twopass.merge150.wgt10.zgt2.wig.gz +UW.IMR90.ChromatinAccessibility.DS11764.twopass.merge150.wgt10.zgt2.wig.gz UW DHS IMR90 Lung IMR90 NA GSM468801 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.IMR90.ChromatinAccessibility.DS11764.twopass.merge150.wgt10.zgt2.wig.gz +UW.IMR90.ChromatinAccessibility.DS13219.twopass.merge150.wgt10.zgt2.wig.gz UW DHS IMR90 Lung IMR90 NA GSM530665 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.IMR90.ChromatinAccessibility.DS13219.twopass.merge150.wgt10.zgt2.wig.gz +UW.IMR90.ChromatinAccessibility.DS13229.twopass.merge150.wgt10.zgt2.wig.gz UW DHS IMR90 Lung IMR90 NA GSM530666 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.IMR90.ChromatinAccessibility.DS13229.twopass.merge150.wgt10.zgt2.wig.gz +UW.iPS_DF_19.11.ChromatinAccessibility.DS15153.twopass.merge150.wgt10.zgt2.wig.gz UW DHS iPS_DF_19.11 IPS cell iPS_DF_19.11 NA GSM665801 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.iPS_DF_19.11.ChromatinAccessibility.DS15153.twopass.merge150.wgt10.zgt2.wig.gz +UW.iPS_DF_19.7.ChromatinAccessibility.DS15148.twopass.merge150.wgt10.zgt2.wig.gz UW DHS iPS_DF_19.7 IPS cell iPS_DF_19.7 NA GSM665800 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.iPS_DF_19.7.ChromatinAccessibility.DS15148.twopass.merge150.wgt10.zgt2.wig.gz +UW.iPS_DF_4.7.ChromatinAccessibility.DS15169.twopass.merge150.wgt10.zgt2.wig.gz UW DHS iPS_DF_4.7 IPS cell iPS_DF_4.7 NA GSM665803 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.iPS_DF_4.7.ChromatinAccessibility.DS15169.twopass.merge150.wgt10.zgt2.wig.gz +UW.iPS_DF_6.9.ChromatinAccessibility.DS15164.twopass.merge150.wgt10.zgt2.wig.gz UW DHS iPS_DF_6.9 IPS cell iPS_DF_6.9 NA GSM665802 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.iPS_DF_6.9.ChromatinAccessibility.DS15164.twopass.merge150.wgt10.zgt2.wig.gz +UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_00738.DS13199.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_00738+ Blood CD34_Mobilised; RO_00738+ GSM530664 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_00738.DS13199.twopass.merge150.wgt10.zgt2.wig.gz +UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01480.DS12771.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01480+ Blood CD34_Mobilised; RO_01480+ GSM530658 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/ERC_hotspots/UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01480.DS12771.twopass.merge150.wgt10.zgt2.wig.gz +UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01492.DS12774.twopass.merge150.wgt10.zgt2.wig.gz UW DHS Mobilized_CD34_Primary_Cells.RO_01492+ Blood CD34_Mobilised; RO_01492+ GSM530659 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http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E091-DNase.hotspot.fdr0.01.broad.bed.gz +E092-DNase.hotspot.fdr0.01.broad.bed UW DHS E092 Fetal Stomach Fetal Stomach E092 Fetal Stomach NA E092 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E092-DNase.hotspot.fdr0.01.broad.bed.gz +E093-DNase.hotspot.fdr0.01.broad.bed UW DHS E093 Fetal Thymus Fetal Thymus E093 Fetal Thymus NA E093 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E093-DNase.hotspot.fdr0.01.broad.bed.gz +E094-DNase.hotspot.fdr0.01.broad.bed UW DHS E094 Gastric Gastric E094 Gastric NA E094 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E094-DNase.hotspot.fdr0.01.broad.bed.gz +E097-DNase.hotspot.fdr0.01.broad.bed UW DHS E097 Ovary Ovary E097 Ovary NA E097 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E097-DNase.hotspot.fdr0.01.broad.bed.gz +E098-DNase.hotspot.fdr0.01.broad.bed UW DHS E098 Pancreas Pancreas E098 Pancreas NA E098 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E098-DNase.hotspot.fdr0.01.broad.bed.gz +E100-DNase.hotspot.fdr0.01.broad.bed UW DHS E100 Psoas Muscle Psoas Muscle E100 Psoas Muscle NA E100 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E100-DNase.hotspot.fdr0.01.broad.bed.gz +E109-DNase.hotspot.fdr0.01.broad.bed UW DHS E109 Small Intestine Small Intestine E109 Small Intestine NA E109 http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/broadPeak/DNase/E109-DNase.hotspot.fdr0.01.broad.bed.gz \ No newline at end of file diff --git a/database/init_db.pl b/database/init_db.pl new file mode 100644 index 0000000..b431989 --- /dev/null +++ b/database/init_db.pl @@ -0,0 +1,112 @@ +#! /usr/bin/env perl +use strict; +use warnings; + +use DBI; +use Getopt::Long; + +my $db_dir = "."; +my $db_name = "eforge_1.1.db"; + + +my $help; + +my $desc = qq{init_db.pl [--db_name $db_name] [--db_dir $db_dir] + +where: + --db_name is the name of the SQLite file [def: $db_name] + --db_dir is the location of the SQLite file [def: $db_dir] + +}; + +GetOptions( + "help" => \$help, + "db_name=s" => \$db_name, + "db_dir=s" => \$db_dir, + ); + +if ($help) { + print $desc; + exit(0); +} + +my $dsn = "dbi:SQLite:dbname=$db_dir/$db_name"; +my $dbh = DBI->connect($dsn, "", "") or die $DBI::errstr; + + +$dbh->do("CREATE TABLE IF NOT EXISTS assembly ( + assembly_id INTEGER PRIMARY KEY AUTOINCREMENT, + species_name, + assembly_name, + UNIQUE (species_name, assembly_name))"); + + +$dbh->do("CREATE TABLE IF NOT EXISTS array ( + array_id INTEGER PRIMARY KEY AUTOINCREMENT, + array_tag UNIQUE, + array_name UNIQUE, + species_name)"); +$dbh->do("CREATE TABLE IF NOT EXISTS probe_mapping_info ( + probe_mapping_id INTEGER PRIMARY KEY AUTOINCREMENT, + array_id INTEGER NOT NULL REFERENCES array(array_id), + assembly_id INTEGER NOT NULL, + url, + UNIQUE (array_id, assembly_id))"); +$dbh->do("CREATE TABLE IF NOT EXISTS probe_mapping ( + probe_mapping_id INTEGER NOT NULL REFERENCES probe_mapping_info(probe_mapping_id), + probe_id, + chr_name, + position INTEGER, + UNIQUE (probe_mapping_id, probe_id))"); +$dbh->do("CREATE INDEX probe_mapping_idx1 on probe_mapping (position, chr_name)"); + + +$dbh->do("CREATE TABLE IF NOT EXISTS proxy_filter_info ( + array_id INTEGER NOT NULL REFERENCES array(array_id), + description, + UNIQUE(array_id))"); +$dbh->do("CREATE TABLE IF NOT EXISTS proxy_filter ( + proxy_filter_id INTEGER NOT NULL REFERENCES proxy_filter_info(proxy_filter_id), + probe_id, + proxy_probes, + UNIQUE (proxy_filter_id, probe_id))"); + + +$dbh->do("CREATE TABLE IF NOT EXISTS probe_annotation_info ( + array_id INTEGER NOT NULL REFERENCES array(array_id), + gene_reference_name NOT NULL, + cgi_reference_name NOT NULL, + url, + UNIQUE(array_id))"); +$dbh->do("CREATE TABLE IF NOT EXISTS probe_annotation ( + array_id INTEGER NOT NULL REFERENCES probe_annotation_info(array_id), + probe_id NOT NULL, + gene_group, + cgi_group, + UNIQUE (array_id, probe_id))"); + + +$dbh->do("CREATE TABLE IF NOT EXISTS dataset ( + dataset_id INTEGER PRIMARY KEY AUTOINCREMENT, + dataset_tag UNIQUE, + dataset_name UNIQUE, + species_name)"); +$dbh->do("CREATE TABLE IF NOT EXISTS sample ( + dataset_id INTEGER REFERENCES dataset(dataset_id), + sample_order INTEGER, + file, + lab, + datatype, + cell, + tissue, + shortcell, + individual, + acc, + url)"); +$dbh->do("CREATE TABLE IF NOT EXISTS probe_bitstring ( + array_id INTEGER NOT NULL REFERENCES array(array_id), + probe_id INTEGER NOT NULL, + dataset_id INTEGER NOT NULL REFERENCES dataset(dataset_id), + sum INTEGER, + bit, + UNIQUE(array_id,probe_id,dataset_id))"); diff --git a/database/load_450k_array.pl b/database/load_450k_array.pl new file mode 100644 index 0000000..65ff62d --- /dev/null +++ b/database/load_450k_array.pl @@ -0,0 +1,286 @@ +#! /usr/bin/env perl +use strict; +use warnings; + +use Getopt::Long; +use File::Spec qw(splitpath); +use DBI; + +my $db_dir = "."; +my $db_name = "eforge_1.1.db"; +my $array_tag = "450k"; +my $array_name = "Illumina Human 450k array"; +my $species = "Homo sapiens"; +my $proxy_threshold = 1000; +my $illumina450k_csv_file = 'ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/ProductFiles/HumanMethylation450/HumanMethylation450_15017482_v1-2.csv'; +my $work_dir = "."; +my $bedtools = "bedtools"; + +my $help; + +my $desc = qq{load_450k_array.pl [options] + +DESCRIPTION: + +This script loads the probe locations and annotations of the Illumina Human 450k methylation array +into the eFORGE database. + +Note that you *must* load the arrays before loading the datasets. If you want to include new arrays +at a later date, you will have to reload all the datasets again (i.e. you will have to re-start from +scratch). + +Optional arguments: + --db_name <name> + is the name of the SQLite file [def: $db_name] + --db_dir <path> + is the location of the SQLite file [def: $db_dir] + --work_dir <path> + is the location where temporary files will be downloaded/created [def: $work_dir] + --bedtools <name> + is the name of the bedtools executable you want to use [def: $bedtools] +}; + +GetOptions( + "help" => \$help, + "db_name=s" => \$db_name, + "db_dir=s" => \$db_dir, + "work_dir=s" => \$work_dir, + "bedtools=s" => \$bedtools, + ); + +my $dsn = "dbi:SQLite:dbname=$db_dir/$db_name"; +my $dbh = DBI->connect($dsn, "", "") or die $DBI::errstr; + +my ($vol, $apth, $file) = File::Spec->splitpath($illumina450k_csv_file); + +if (!-e "$work_dir/$file") { + download_url($illumina450k_csv_file, $work_dir); +} + +my $array_info = parse_450k_file("$work_dir/$file"); + +load_array($dbh, $db_name, $species, $array_tag, $array_name, $array_info); + +load_proxy_filter($dbh, $db_name, $array_tag, "GRCh37", $work_dir, $proxy_threshold); + +exit(); + + +sub download_url { + my ($url, $work_dir) = @_; + + print "Downloading $url...\n"; + system("wget -q -N -P $work_dir $url"); +} + + +sub parse_450k_file { + my ($illumina450k_csv_file) = @_; + my $array; + + open(CSV, $illumina450k_csv_file) or die; + my $annotation; + my @gene_annotations = ("TSS200", "TSS1500", "1stExon", "Body", "3'UTR", "5'UTR", "IGR"); + my $cpg_annotations = { + 'N_Shelf' => "Shelf_Shore", + 'S_Shelf' => "Shelf_Shore", + 'N_Shore' => "Shelf_Shore", + 'S_Shore' => "Shelf_Shore", + 'Island' => "Island"}; + while (<CSV>) { + chomp; + my @data = split(",", $_); + my $probe_id = $data[0]; + next if ($probe_id !~ /^cg/ and $probe_id !~ /^ch\./); + my $probe_chr37 = $data[11]; + my $probe_loc37 = $data[12]; + my $probe_chr36 = $data[14]; + my $probe_loc36 = $data[15]; + my $this_gene_annotation_arrayStr = $data[23]; + my $this_cpg_annotation = $data[25]?$cpg_annotations->{$data[25]}:"NA"; + + my $this_gene_annotation; + if (!defined($this_gene_annotation_arrayStr) or $this_gene_annotation_arrayStr eq "") { + $this_gene_annotation = "IGR"; + } else { + my @this_gene_annotations = split(";", $this_gene_annotation_arrayStr); + foreach my $this_a (@this_gene_annotations) { + if (grep {$_ eq $this_a} @gene_annotations) { + $this_gene_annotation = $this_a; + last; + } + } + } + + $annotation->{$this_gene_annotation."-".$this_cpg_annotation}++; + + $array->{$probe_id} = [$probe_chr36, $probe_loc36, $probe_chr37, $probe_loc37, $this_gene_annotation, $this_cpg_annotation]; + } +# foreach my $this_a (keys %$annotation) { #@gene_annotations) { +# print $annotation->{$this_a}, "\t", $this_a, "\n"; +# } + + return $array; +} + + +sub load_array_1 { + my ($dbh, $code_name, $array_info) = @_; + + my $table_name = $code_name; + $table_name =~ s/\W//g; + $table_name = "array_$table_name"; + $dbh->do("CREATE TABLE IF NOT EXISTS $table_name (probe_id, location, gene_group, cgi_group)"); + + my $sth = $dbh->prepare("INSERT INTO array_$code_name VALUES (?, ?, ?, ?)"); + foreach my $this_probe_id (sort keys $array_info) { + my ($chr, $loc, $gene_group, $cgi_group) = @{$array_info->{$this_probe_id}}; + my $location = "$chr:$loc-$loc"; + $sth->execute($this_probe_id, $location, $gene_group, $cgi_group); + } + $sth->finish(); + + return $table_name; +} + + +sub load_array { + my ($dbh, $db_name, $species_name, $array_tag, $array_name, $array_info) = @_; + + my $sth; + $sth = $dbh->prepare("INSERT OR IGNORE INTO array (array_tag, array_name, species_name) VALUES (?, ?, ?)"); + $sth->execute($array_tag, $array_name, $species_name); + my $array_id = $dbh->last_insert_id("", "", "", ""); + $sth->finish(); + if ($array_id == 0) { + $array_id = $dbh->selectrow_array("SELECT array_id FROM array WHERE array_name = '$array_name' AND species_name = 'Homo sapiens'"); + } + + $sth = $dbh->prepare("INSERT OR IGNORE INTO assembly (species_name, assembly_name) VALUES (?, ?)"); + $sth->execute($species_name, "GRCh37"); + $sth->execute($species_name, "NCBI36"); + $sth->finish(); + my $human36_assembly_id = $dbh->selectrow_array("SELECT assembly_id FROM assembly WHERE species_name = 'Homo sapiens' AND assembly_name = 'NCBI36'"); + my $human37_assembly_id = $dbh->selectrow_array("SELECT assembly_id FROM assembly WHERE species_name = 'Homo sapiens' AND assembly_name = 'GRCh37'"); + + $sth = $dbh->prepare("INSERT OR IGNORE INTO probe_mapping_info (array_id, assembly_id, url) VALUES (?, ?, ?)"); + $sth->execute($array_id, $human36_assembly_id, ""); + my $probe_mapping_human36_id = $dbh->last_insert_id("", "", "", ""); + $sth->execute($array_id, $human37_assembly_id, ""); + my $probe_mapping_human37_id = $dbh->last_insert_id("", "", "", ""); + $sth->finish(); + + $sth = $dbh->prepare("INSERT OR IGNORE INTO probe_annotation_info (array_id, gene_reference_name, cgi_reference_name, url) VALUES (?, ?, ?, ?)"); + $sth->execute($array_id, "RefSeq", "UCSC CpG Islands", ""); +# my $probe_annotation_id = $dbh->last_insert_id("", "", "", ""); + $sth->finish(); + + open(CSV1, ">probe_mapping.csv") or die; + open(CSV2, ">probe_annotation.csv") or die; +# my $sth1 = $dbh->prepare("INSERT OR IGNORE INTO probe_mapping (probe_mapping_id, probe_id, chr_name, position) VALUES (?, ?, ?, ?)"); +# my $sth2 = $dbh->prepare("INSERT OR IGNORE INTO probe_annotation (probe_annotation_id, probe_id, gene_group, cgi_group) VALUES (?, ?, ?, ?)"); + foreach my $this_probe_id (sort keys $array_info) { + my ($chr36, $loc36, $chr37, $loc37, $gene_group, $cgi_group) = @{$array_info->{$this_probe_id}}; + print CSV1 join(",", $probe_mapping_human36_id, $this_probe_id, "chr$chr36", $loc36), "\n"; + print CSV1 join(",", $probe_mapping_human37_id, $this_probe_id, "chr$chr37", $loc37), "\n"; +# print CSV2 join(",", $probe_annotation_id, $array_id, $this_probe_id, $gene_group, $cgi_group), "\n"; + print CSV2 join(",", $array_id, $this_probe_id, $gene_group, $cgi_group), "\n"; +# $sth1->execute($probe_mapping_human36_id, $this_probe_id, "chr$chr36", $loc36) if ($probe_mapping_human36_id); +# $sth1->execute($probe_mapping_human37_id, $this_probe_id, "chr$chr37", $loc37) if ($probe_mapping_human37_id); +# $sth2->execute($probe_annotation_id, $this_probe_id, $gene_group, $cgi_group) if ($probe_annotation_id); + } + close(CSV1); + close(CSV2); + system("echo '.mode csv +.import probe_mapping.csv probe_mapping +.import probe_annotation.csv probe_annotation' | sqlite3 $db_name"); +# $sth1->finish(); +# $sth2->finish(); + +} + +sub load_proxy_filter { + my ($dbh, $db_name, $array_tag, $assembly_name, $work_dir, $distance_threshold) = @_; + + my $array_id = $dbh->selectrow_arrayref("SELECT array_id FROM array WHERE array_tag = '$array_tag'")->[0]; + my $bed_file = dump_array_bed_file($dbh, $array_id, $assembly_name, $work_dir); + my $this_output_bed_file = "$work_dir/array_${array_id}.proxy.bed"; + my $runstr = "$bedtools window -w $distance_threshold -a $bed_file -b $bed_file > $this_output_bed_file"; + system($runstr) == 0 or die "Error while running bedtools: $?"; + + my $sth = $dbh->prepare("INSERT OR IGNORE INTO proxy_filter_info (array_id, description) VALUES (?, ?)"); + $sth->execute($array_id, "Distance-based: 1kb"); + + open(BED, $this_output_bed_file) or die; + my $all_probes; + my $mapping_probes; + while (<BED>) { + chomp; + my ($chr1, $start1, $end1, $probe1, $chr2, $start2, $end2, $probe2) = split("\t", $_); + $all_probes->{$probe1} = 1; + if ($probe1 ne $probe2) { + $mapping_probes->{$probe1}->{$probe2} = 1; + } + } + close(BED); + open(CSV, ">proxy_filter.csv") or die; + foreach my $probe (sort keys %$all_probes) { + if (defined($mapping_probes->{$probe})) { + print CSV "$array_id,$probe,", join("|", sort keys %{$mapping_probes->{$probe}}), "\n"; + } else { + print CSV "$array_id,$probe,NONE\n"; + } + } + close(CSV); + system("echo '.mode csv +.import proxy_filter.csv proxy_filter' | sqlite3 $db_name"); + +} + +sub dump_array_bed_file { + my ($dbh, $this_array_id, $assembly_name, $work_dir) = @_; + my $sql = "SELECT probe_mapping_id + FROM probe_mapping_info + JOIN assembly USING (assembly_id) + WHERE array_id = $this_array_id + AND assembly_name = '$assembly_name'"; + my $probe_mapping_id = $dbh->selectrow_array($sql); + if (!$probe_mapping_id) { + die "Cannot find a mapping for array $this_array_id and assembly $assembly_name\n"; + } + + $sql = "SELECT probe_id, chr_name, position FROM probe_mapping WHERE probe_mapping_id = $probe_mapping_id"; + my $probes = $dbh->selectall_arrayref($sql); + + my $bed_file = "$work_dir/array_${this_array_id}.bed"; + open(BED, ">$bed_file") or die; + foreach my $this_probe (sort _sort_probes @$probes) { + print BED join("\t", $this_probe->[1], $this_probe->[2], $this_probe->[2]+1, $this_probe->[0]), "\n"; + } + close(BED); + + return $bed_file; +} + +sub _sort_probes { + my $chr_a = $a->[1]; + my $chr_b = $b->[1]; + my $loc_a = $a->[2]; + my $loc_b = $b->[2]; + $chr_a =~ s/chr//; + $chr_b =~ s/chr//; + if ($chr_a eq $chr_b) { + return $loc_a <=> $loc_b; + } elsif ($chr_a =~ /^\d/ and $chr_b =~ /^\d/) { + return $chr_a <=> $chr_b; + } elsif ($chr_a =~ /^\d/) { + return -1; + } elsif ($chr_b =~ /^\d/) { + return 1; + } else { + return $chr_a cmp $chr_b; + } +} + + +exit(); diff --git a/database/load_dataset.pl b/database/load_dataset.pl new file mode 100644 index 0000000..c984b0c --- /dev/null +++ b/database/load_dataset.pl @@ -0,0 +1,415 @@ +#! /usr/bin/env perl +use strict; +use warnings; + +use Getopt::Long; +use DBI; + +my $db_dir = "."; +my $db_name = "eforge_1.1.db"; +my $dataset_name = "ENCODE"; +my $dataset_tag = "encode"; +my $decode_file = "encode.decode"; +my $work_dir = "/tmp"; +my $species_name = "Homo sapiens"; +my $assembly_name = "GRCh37"; +my $bedtools = "bedtools"; + +my $help; + +my $desc = qq{load_dataset.pl [options] + +DESCRIPTION: + +This script reads a 'decode' file which contains references to a list of samples, each of them +corresponding to a given dataset. Each of these files is a BED or BED-like file that is read by +bedtools to find overlaps with each and every array loaded in the eFORGE database. + +Note that you *must* load the arrays first. If you want to include new arrays at a later date, you +will have to reload all the datasets again (i.e. you will have to re-start from scratch). + +Required parameters: + --tag <tag> or --dataset_tag <tag> + the ID for this database. This needs to be unique. + --name <name> or --dataset_name <name> + the name for this database. This can be a longer description. It will be used in the web interface. + --decode_file <file> + the file with the information about each sample in this dataset + +Optional parameters: + --db_name <name> + is the name of the SQLite file [def: $db_name] + --db_dir <path> + is the location of the SQLite file [def: $db_dir] + --work_dir <path> + is the location where temporary files will be downloaded/created [def: $work_dir] + --bedtools <name> + is the name of the bedtools executable you want to use [def: $bedtools] + --species <species> + is the name of the species [def: $species_name] + --assembly <assembly> + is the name of the assembly [def: $assembly_name] +}; + +GetOptions( + "help" => \$help, + "db_name=s" => \$db_name, + "db_dir=s" => \$db_dir, + "tag|dataset_tag=s" => \$dataset_tag, + "name|dataset_name=s" => \$dataset_name, + "decode_file=s" => \$decode_file, + "work_dir=s" => \$work_dir, + "species=s" => \$species_name, + "assembly=s" => \$assembly_name, + ); + +if ($help) { + print $desc; + exit(0); +} + +my $dsn = "dbi:SQLite:dbname=$db_dir/$db_name"; +my $dbh = DBI->connect($dsn, "", "") or die $DBI::errstr; + +system("mkdir -p $work_dir"); + +my $decode_table = get_decode_table($decode_file); + +my $dataset_id = load_dataset($dbh, $species_name, $decode_table, $dataset_name, $dataset_tag); + +download_bed_files($decode_table, $work_dir); + +my $arrays = get_all_arrays_for_species($dbh, $species_name); + +foreach my $this_array (@$arrays) { + my ($this_array_id, $this_array_name) = @$this_array; + my $sorted_array_bed_file = dump_array_bed_file($dbh, $this_array_id, $assembly_name, $work_dir); + my $single_overlaps_bed_files = run_single_overlap_bedtools($bedtools, $work_dir, $sorted_array_bed_file, $decode_table, $this_array_id, $this_array_name); + my $concatenated_overlaps_bed_file = paste_files($single_overlaps_bed_files, $work_dir, $this_array_id); + my $final_overlaps_bed_file = add_sum_column_to_concatenated_bedfile($concatenated_overlaps_bed_file, $work_dir, $this_array_id); + load_bitstrings($dbh, $db_name, $final_overlaps_bed_file, $this_array_id, $dataset_id); +} + +# + + +exit(); + +my $input_bed_files = get_input_bed_files_from_decode_table($decode_file); + +exit(0); + +sub load_dataset { + my ($dbh, $species_name, $decode_table, $dataset_name) = @_; + my $dataset_id; + + my $sth; + $sth = $dbh->prepare("INSERT OR IGNORE INTO dataset (dataset_tag, dataset_name, species_name) VALUES (?, ?, ?)"); + $sth->execute($dataset_tag, $dataset_name, $species_name); + $dataset_id = $dbh->last_insert_id("", "", "", ""); + $sth->finish(); + if ($dataset_id == 0) { + $dataset_id = $dbh->selectrow_array("SELECT dataset_id FROM dataset WHERE dataset_name = '$dataset_name' AND species_name = '$species_name'"); + } + + + $sth = $dbh->prepare("INSERT OR IGNORE INTO sample (dataset_id, sample_order, file, lab, datatype, cell, tissue, shortcell, individual, acc, url) + VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)"); + my $sample_order = 1; + foreach my $this_sample (@$decode_table) { + $sth->execute($dataset_id, + $sample_order, + $this_sample->{file}, + $this_sample->{lab}, + $this_sample->{datatype}, + $this_sample->{cell}, + $this_sample->{tissue}, + $this_sample->{shortcell}, + $this_sample->{individual}, + $this_sample->{acc}, + $this_sample->{url}); + $sample_order++; + } + + return($dataset_id); +} + +sub load_bitstrings { + my ($dbh, $db_name, $bed_file, $array_id, $dataset_id) = @_; + +# my $sql = "INSERT INTO probe_bitstring (array_id, probe_id, dataset_id, sum, bit) +# VALUES (?, ?, ?, ?, ?)"; +# my $sth = $dbh->prepare($sql); + open(BED, $bed_file) or die "Cannot open BED file <$bed_file>\n"; + open(CSV, ">probe_bitstring.csv") or die "Cannot open CVS temporary file <probe_bitstring.csv>\n"; + while(<BED>) { + chomp; + my ($chr, $start, $end, $probe_id, $sum, $bitstring) = split("\t", $_); + print CSV join(",", $array_id, $probe_id, $dataset_id, $sum, $bitstring), "\n"; +# $sth->execute($array_id, $probe_id, $dataset_id, $sum, $bitstring); + } + close(BED); + close(CSV); + system("echo '.mode csv +.import probe_bitstring.csv probe_bitstring' | sqlite3 $db_name"); +# $sth->finish(); +} + +=head2 add_sum_column_to_concatenated_bedfile + + Arg[1] : string $concatenated_overlaps_bed_file (location of the input BED file with 0/1 flags on the 4th column) + Arg[2] : string $work_dir (where to put the temporary files) + Example : my $final_overlaps_bed_file = add_sum_column_to_concatenated_bedfile($concatenated_overlaps_bed_file, $work_dir); + Description : Reads the input BED file ($concatenated_overlaps_bed_file) which contains a series + of 0 and 1 flags in the 4th column. This function reads the number of ones in that + column and include that value in the output BED file. The output BED file will + contain that number in the 4th column and the series of flag in the 5th colum. + Returns : string $final_overlaps_bed_file (the location of the resulting BED file) + Exceptions : Dies if error when opening the files + +=cut + +sub add_sum_column_to_concatenated_bedfile { + my ($concatenated_overlaps_bed_file, $work_dir, $array_id) = @_; + my $final_overlaps_bed_file = "$work_dir/final_overlaps.array_${array_id}.bed"; + + open(BED_IN, $concatenated_overlaps_bed_file) or die "Cannot open BED file <$concatenated_overlaps_bed_file>\n"; + open(BED_OUT, ">$final_overlaps_bed_file") or die "Cannot open BED file <$final_overlaps_bed_file>\n"; + while(<BED_IN>) { + chomp; + my ($this_chr, $this_start, $this_end, $this_probe, $this_bitstring) = split("\t", $_); + my $num = $this_bitstring =~ tr/1/1/; + print BED_OUT join("\t", $this_chr, $this_start, $this_end, $this_probe, $num, $this_bitstring), "\n"; + } + close(BED_IN); + close(BED_OUT); + + return $final_overlaps_bed_file; +} + + +=head2 run_single_overlap_bedtools + + Arg[1] : string $bedtools (either full path or just the binary if in the $PATH) + Arg[2] : string $work_dir (where to put the temporary files) + Arg[3] : string $sorted_450k_bed_file (location of the BED file with sorted 450K features) + Arg[4] : arrayref of hash $decode_table + Example : my $single_overlaps_bed_files = run_single_overlap_bedtools($bedtools, $work_dir, $sorted_450k_bed_file, $decode_table); + Description : Run bedtools on the sorted 450K features vs all the BED DNAse features, one at a time. + Returns : arrayref of string $total_overlaps_bed_files (the locations of the resulting BED files) + Exceptions : Dies if error when running bedtools + +=cut + +sub run_single_overlap_bedtools { + my ($bedtools, $work_dir, $sorted_array_bed_file, $decode_table, $array_id, $array_name) = @_; + my $single_overlap_bed_files = []; + + foreach my $this_input_bed_file (map {$_->{"file"}} @$decode_table) { + print "Overlap between $array_name and $this_input_bed_file...\n"; + my $this_output_bed_file = $this_input_bed_file; + $this_output_bed_file =~ s/.+\///; + $this_output_bed_file = "$work_dir/single_overlaps.array_${array_id}.$this_output_bed_file"; + my $runstr = "$bedtools intersect -c -a $sorted_array_bed_file -b $work_dir/$this_input_bed_file > $this_output_bed_file"; + system($runstr) == 0 or die "Error while running bedtools: $?"; + push(@$single_overlap_bed_files, $this_output_bed_file); + } + + return $single_overlap_bed_files; +} + + +sub get_decode_table { + my ($decode_file) = @_; + my $decode_table; + + open(DECODE, $decode_file) or die "Cannot open decode file <$decode_file>\n"; + my $whole_text = join("\n", <DECODE>); + $whole_text =~ s/[\r\n]+/\n/g; + my @lines = split("\n", $whole_text); + close(DECODE); + + my @header = split("\t", shift(@lines)); + + foreach my $this_line (@lines) { + my @data = split("\t", $this_line); + my $decode_record = {}; + for (my $i=0; $i<@header; $i++) { + $decode_record->{$header[$i]} = $data[$i]; + } + # Check that file and URL match + die $this_line if ($decode_record->{"url"} !~ $decode_record->{"file"}); + $decode_record->{"file"} = $decode_record->{"url"}; + $decode_record->{"file"} =~ s/.+\///g; + push(@$decode_table, $decode_record); + } + + return $decode_table; +} + +sub download_bed_files { + my ($decode_table, $work_dir) = @_; + + foreach my $this_decode_entry (@$decode_table) { + my $url = $this_decode_entry->{"url"}; + my $file = $this_decode_entry->{"file"}; + if (!-e "$work_dir/$file") { + download_url($url, $work_dir); + } + } +} + + +sub download_url { + my ($url, $work_dir) = @_; + + print "Downloading $url...\n"; + system("wget", "-q", "-N", "-P", $work_dir, $url) == 0 + or die "Error: wget -q -N -P $work_dir $url\n$!"; +} + + +sub paste_files { + my ($files, $work_dir, $array_id) = @_; + my $output_file = "$work_dir/concat_overlaps.array_${array_id}.bed"; + + my $max_num_files = 200; + my $c = 0; + my $temp_output_file; + my @original_files = @$files; + while (@$files > 1) { + $c++; + $temp_output_file = "$work_dir/temp.$$.$c.paste_files.txt"; + my $input_files = [splice(@$files, 0, $max_num_files)]; +# print STDERR "Merging ", join(", ", @$input_files), " into $temp_output_file\n"; + merge_files($temp_output_file, $input_files); + unshift(@$files, $temp_output_file); + } + rename($temp_output_file, $output_file); + + unlink glob "$work_dir/temp.$$.*.paste_files.txt"; + +# +# +# +# +# unlink @original_files; +# +# +# +# + + return $output_file; +} + + +sub merge_files { + my ($output_file, $input_files) = @_; + my @fhs; + my $c = 0; + + foreach my $this_input_file (@$input_files) { + open($fhs[$c++], $this_input_file) or die "Cannot open $this_input_file: $!\n"; + } + open(OUT, ">$output_file") or die "Cannot open $output_file: $!\n"; + + my $first_fh = shift(@fhs); + + while (1) { + my $line = <$first_fh>; + chomp($line); + my ($chr, $start, $end, $probe_id, $value) = split("\t", $line); + print OUT join("\t", $chr, $start, $end, $probe_id, $value); + foreach my $this_fh (@fhs) { + my $line = <$this_fh>; + chomp($line); + my ($this_chr, $this_start, $this_end, $this_probe_id, $this_value) = split("\t", $line); + if (($this_chr ne $chr) or ($this_start != $start) or ($this_end != $end) or ($this_probe_id ne $probe_id)) { + die "Files do not contain the same $chr-$start-$end-$probe_id lines\n"; + } + print OUT $this_value; + } + print OUT "\n"; + if (eof($first_fh)) { + last; + } + } + + foreach my $this_fh (@fhs) { + close($this_fh); + } + close(OUT); +} + +sub get_all_arrays_for_species { + my ($dbh, $species) = @_; + my $arrays; + + my $sth = $dbh->prepare("SELECT array_id, array_name FROM array WHERE species_name = ?"); + $sth->execute($species); + $arrays = $sth->fetchall_arrayref(); + $sth->finish(); + + return $arrays; +} + +sub get_probe_mapping_id { + my ($dbh, $this_array_id, $assembly_name) = @_; + my $sql = "SELECT probe_mapping_id + FROM probe_mapping_info + JOIN assembly USING (assembly_id) + WHERE array_id = $this_array_id + AND assembly_name = '$assembly_name'"; + my $probe_mapping_id = $dbh->selectrow_array($sql); + return($probe_mapping_id); +} + +sub dump_array_bed_file { + my ($dbh, $this_array_id, $assembly_name, $work_dir) = @_; + my $sql = "SELECT probe_mapping_id + FROM probe_mapping_info + JOIN assembly USING (assembly_id) + WHERE array_id = $this_array_id + AND assembly_name = '$assembly_name'"; + my $probe_mapping_id = $dbh->selectrow_array($sql); + + $sql = "SELECT probe_id, chr_name, position FROM probe_mapping WHERE probe_mapping_id = $probe_mapping_id"; + my $probes = $dbh->selectall_arrayref($sql); + + my $bed_file = "$work_dir/array_${this_array_id}.bed"; + open(BED, ">$bed_file") or die "Cannot open temporary BED file <$bed_file>\n"; + foreach my $this_probe (sort _sort_probes @$probes) { + print BED join("\t", $this_probe->[1], $this_probe->[2], $this_probe->[2]+1, $this_probe->[0]), "\n"; + } + close(BED); + + return $bed_file; +} + +sub _sort_probes { + my $chr_a = $a->[1]; + my $chr_b = $b->[1]; + my $loc_a = $a->[2]; + my $loc_b = $b->[2]; + $chr_a =~ s/chr//; + $chr_b =~ s/chr//; + if ($chr_a eq $chr_b) { + return $loc_a <=> $loc_b; + } elsif ($chr_a =~ /^\d/ and $chr_b =~ /^\d/) { + return $chr_a <=> $chr_b; + } elsif ($chr_a =~ /^\d/) { + return -1; + } elsif ($chr_b =~ /^\d/) { + return 1; + } else { + return $chr_a cmp $chr_b; + } +} + +exit(); + + + + + + From 4e5fbee54e65b59f328403e299026ee00f073081 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Wed, 30 Sep 2015 11:34:51 +0100 Subject: [PATCH 09/26] Use SQL query compatible with old RDBM --- eForge/eForge.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/eForge/eForge.pm b/eForge/eForge.pm index 2e2a571..7121134 100644 --- a/eForge/eForge.pm +++ b/eForge/eForge.pm @@ -418,7 +418,7 @@ sub get_bits{ FROM probe_annotation JOIN probe_bitstring USING (array_id, probe_id) JOIN dataset USING (dataset_id) - JOIN array USING (array_id) + JOIN array ON (array.array_id = probe_annotation.array_id) WHERE array_tag = ? and dataset_tag = ? AND probe_id IN (?". (",?" x ($end - $start)).")"; my $sth = $dbh->prepare_cached($sql); #get the blocks form the ld table From e65293db316c95eba65df328816cd01a57d63414 Mon Sep 17 00:00:00 2001 From: Javier Herrero <jherrero@users.noreply.github.com> Date: Wed, 30 Sep 2015 16:23:17 +0100 Subject: [PATCH 10/26] Update AUTHORS --- AUTHORS | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/AUTHORS b/AUTHORS index 16a081a..3189fd0 100644 --- a/AUTHORS +++ b/AUTHORS @@ -1,3 +1,3 @@ -eFORGE was initially developed by Charles Breeze while on secondment at the European Bioinformatics Institute as part of the EpiTrain Initial Training Network. +eFORGE was developed by Charles Breeze while on secondment at the European Bioinformatics Institute as part of the EpiTrain Initial Training Network. The code, webserver and database are currently maintained by Charles Breeze and Javier Herrero. From 13c699b7ef7567235ee9dd3760eb9cdaa1ab825c Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Wed, 30 Sep 2015 22:29:06 +0100 Subject: [PATCH 11/26] Change file to UNIX file format --- database/encode.decode | 127 ++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 126 insertions(+), 1 deletion(-) diff --git a/database/encode.decode b/database/encode.decode index f205e22..3e67025 100644 --- a/database/encode.decode +++ b/database/encode.decode @@ -1 +1,126 @@ -file lab datatype cell tissue shortcell individual acc url A549-all.twopass.merge150.wgt10.zgt2.wig Combined DHS A549 Epithelium A549 NA "GSM816649,GSM736580,GSM736506" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/A549-all.twopass.merge150.wgt10.zgt2.wig Adult_Th0_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS Adult_CD4+ Blood Adult_CD4+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Adult_Th0_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig AG04449-DS12319.twopass.merge150.wgt10.zgt2.wig UW DHS AG04449 Skin AG04449 NA "GSM736562,GSM736590" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG04449-DS12319.twopass.merge150.wgt10.zgt2.wig AG04450-DS12270.twopass.merge150.wgt10.zgt2.wig UW DHS AG04450 Lung AG04450 NA "GSM736514,GSM736563" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG04450-DS12270.twopass.merge150.wgt10.zgt2.wig AG09309-DS12352.twopass.merge150.wgt10.zgt2.wig UW DHS AG09309 Skin AG09309 NA "GSM736551,GSM736616" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG09309-DS12352.twopass.merge150.wgt10.zgt2.wig AG09319-DS12291.twopass.merge150.wgt10.zgt2.wig UW DHS AG09319 Gingival AG09319 NA "GSM736531,GSM736619" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG09319-DS12291.twopass.merge150.wgt10.zgt2.wig AG10803-DS12384.twopass.merge150.wgt10.zgt2.wig UW DHS AG10803 Skin AG10803 NA "GSM736598,GSM736633" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG10803-DS12384.twopass.merge150.wgt10.zgt2.wig AoAF-DS13523.twopass.merge150.wgt10.zgt2.wig UW DHS AoAF Blood vessel AoAF NA "GSM736583,GSM736505" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AoAF-DS13523.twopass.merge150.wgt10.zgt2.wig BE_2_C-DS14625.twopass.merge150.wgt10.zgt2.wig UW DHS BE2_C Brain BE2_C NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/BE_2_C-DS14625.twopass.merge150.wgt10.zgt2.wig BJ-DS10081.twopass.merge150.wgt10.zgt2.wig UW DHS BJ Skin BJ NA "GSM736518,GSM736596" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/BJ-DS10081.twopass.merge150.wgt10.zgt2.wig CACO2-DS8235.twopass.merge150.wgt10.zgt2.wig UW DHS Caco-2 Colon Caco-2 NA "GSM736500,GSM736587" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CACO2-DS8235.twopass.merge150.wgt10.zgt2.wig CD14-DS18065.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS CD14+ Blood CD14+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CD14-DS18065.hg19.twopass.merge150.wgt10.zgt2.wig CD20-DS17541.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS CD20+ Blood CD20+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CD20-DS17541.hg19.twopass.merge150.wgt10.zgt2.wig CD34-DS16814.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS CD34+ Blood CD34+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CD34-DS16814.hg19.twopass.merge150.wgt10.zgt2.wig CMK-DS12393.twopass.merge150.wgt10.zgt2.wig UW DHS CMK Blood CMK NA GSM736607 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CMK-DS12393.twopass.merge150.wgt10.zgt2.wig E_myoblast_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS E_myoblast Muscle E_myoblast NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/E_myoblast_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig GM06990-DS7748.twopass.merge150.wgt10.zgt2.wig UW DHS GM06990 Blood GM06990 NA "GSM736558,GSM736635" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM06990-DS7748.twopass.merge150.wgt10.zgt2.wig GM12864-DS12431.twopass.merge150.wgt10.zgt2.wig UW DHS GM12864 Blood GM12864 NA GSM736525 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM12864-DS12431.twopass.merge150.wgt10.zgt2.wig GM12865-DS12436.twopass.merge150.wgt10.zgt2.wig UW DHS GM12865 Blood GM12865 NA "GSM736512,GSM736561" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM12865-DS12436.twopass.merge150.wgt10.zgt2.wig GM12878-all.twopass.merge150.wgt10.zgt2.wig Combined DHS GM12878 Blood GM12878 NA "GSM816665,GSM736496,GSM736620" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM12878-all.twopass.merge150.wgt10.zgt2.wig HAc-DS14765.twopass.merge150.wgt10.zgt2.wig UW DHS HAc Cerebellar HAc NA "GSM736586,GSM736538" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAc-DS14765.twopass.merge150.wgt10.zgt2.wig HAEpiC-DS12663.twopass.merge150.wgt10.zgt2.wig UW DHS HAEpiC Epithelium HAEpiC NA "GSM736631,GSM736606" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAEpiC-DS12663.twopass.merge150.wgt10.zgt2.wig HAh-DS15192.twopass.merge150.wgt10.zgt2.wig UW DHS HA-h Brain hippocampus HA-h NA "GSM736594,GSM736535" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAh-DS15192.twopass.merge150.wgt10.zgt2.wig HAsp-DS14790.twopass.merge150.wgt10.zgt2.wig UW DHS HA-sp Spinal cord HA-sp NA "GSM736537,GSM736625" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAsp-DS14790.twopass.merge150.wgt10.zgt2.wig HBMEC-DS13817.twopass.merge150.wgt10.zgt2.wig UW DHS HBMEC Blood vessel HBMEC NA "GSM736509,GSM736554" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HBMEC-DS13817.twopass.merge150.wgt10.zgt2.wig HCFaa-DS13480.twopass.merge150.wgt10.zgt2.wig UW DHS HCFaa Heart HCFaa NA "GSM736494,GSM736601" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCFaa-DS13480.twopass.merge150.wgt10.zgt2.wig HCF-DS12501.twopass.merge150.wgt10.zgt2.wig UW DHS HCF Heart HCF NA "GSM736568,GSM736540" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCF-DS12501.twopass.merge150.wgt10.zgt2.wig HCM-DS12599.twopass.merge150.wgt10.zgt2.wig UW DHS HCM Heart HCM NA "GSM736516,GSM736504" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCM-DS12599.twopass.merge150.wgt10.zgt2.wig HConF-DS11642.twopass.merge150.wgt10.zgt2.wig UW DHS HConF Eye HConF NA "GSM736547,GSM736515" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HConF-DS11642.twopass.merge150.wgt10.zgt2.wig HCPEpiC-DS12447.twopass.merge150.wgt10.zgt2.wig UW DHS HCPEpiC Epithelium HCPEpiC NA "GSM736569,GSM736597" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCPEpiC-DS12447.twopass.merge150.wgt10.zgt2.wig HCT116-DS13551.twopass.merge150.wgt10.zgt2.wig UW DHS HCT-116 Colon HCT-116 NA "GSM736600,GSM736493" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCT116-DS13551.twopass.merge150.wgt10.zgt2.wig HEEpiC-DS12763.twopass.merge150.wgt10.zgt2.wig UW DHS HEEpiC Epithelium HEEpiC NA "GSM736585,GSM736532" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HEEpiC-DS12763.twopass.merge150.wgt10.zgt2.wig Hela-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HeLa-S3 Cervix HeLa-S3 NA "GSM816633,GSM816643,GSM736564,GSM736510" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Hela-all.twopass.merge150.wgt10.zgt2.wig HepG2-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HepG2 Liver HepG2 NA "GSM816662,GSM736637,GSM736639" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HepG2-all.twopass.merge150.wgt10.zgt2.wig HESC-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HESC ES Cell HESC NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HESC-all.twopass.merge150.wgt10.zgt2.wig hESCT0-DS11909.twopass.merge150.wgt10.zgt2.wig UW DHS hESCT0 ES Cell hESCT0 NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/hESCT0-DS11909.twopass.merge150.wgt10.zgt2.wig HFF-DS15115.twopass.merge150.wgt10.zgt2.wig UW DHS HFF Foreskin HFF NA "GSM736602,GSM736572" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HFF-DS15115.twopass.merge150.wgt10.zgt2.wig HFF_MyC-DS15079.twopass.merge150.wgt10.zgt2.wig UW DHS HFF-Myc Foreskin HFF-Myc NA "GSM736524,GSM736605" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HFF_MyC-DS15079.twopass.merge150.wgt10.zgt2.wig HGF-DS11752.twopass.merge150.wgt10.zgt2.wig UW DHS HGF Gingival HGF NA "GSM736579,GSM736576" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HGF-DS11752.twopass.merge150.wgt10.zgt2.wig HIPEpiC-DS12684.twopass.merge150.wgt10.zgt2.wig UW DHS HIPEpiC Epithelium HIPEpiC NA "GSM736589,GSM736615" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HIPEpiC-DS12684.twopass.merge150.wgt10.zgt2.wig HL60-DS11809.twopass.merge150.wgt10.zgt2.wig UW DHS HL-60 Blood HL-60 NA "GSM736626,GSM736595" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HL60-DS11809.twopass.merge150.wgt10.zgt2.wig HMEC-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HMEC Breast HMEC NA "GSM816669,GSM736634,GSM736552" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMEC-all.twopass.merge150.wgt10.zgt2.wig HMF-DS13363.twopass.merge150.wgt10.zgt2.wig UW DHS HMF Breast HMF NA "GSM736628,GSM736541" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMF-DS13363.twopass.merge150.wgt10.zgt2.wig HMVEC_dAd-DS12957.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dAd Blood vessel HMVEC-dAd NA "GSM1024745,GSM1024747" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dAd-DS12957.hg19.twopass.merge150.wgt10.zgt2.wig HMVEC_dBlAd-DS13337.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dBl-Ad Blood vessel HMVEC-dBl-Ad NA "GSM736609,GSM736523" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dBlAd-DS13337.twopass.merge150.wgt10.zgt2.wig HMVEC_dBlNeo-DS13242.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dBl-Neo Blood vessel HMVEC-dBl-Neo NA "GSM736571,GSM736521" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dBlNeo-DS13242.twopass.merge150.wgt10.zgt2.wig HMVEC_dLyAd-DS13261.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dLy-Ad Blood vessel HMVEC-dLy-Ad NA "GSM736599,GSM736591" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dLyAd-DS13261.twopass.merge150.wgt10.zgt2.wig HMVEC_dLyNeo-DS13150.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dLy-Neo Blood vessel HMVEC-dLy-Neo NA "GSM736577,GSM736573" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dLyNeo-DS13150.twopass.merge150.wgt10.zgt2.wig HMVEC_dNeo-DS12937.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dNeo Blood vessel HMVEC-dNeo NA "GSM736611,GSM736624" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dNeo-DS12937.twopass.merge150.wgt10.zgt2.wig HMVEC_LBl-DS13372.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-LBl Blood vessel HMVEC-LBl NA "GSM736542,GSM736511" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_LBl-DS13372.twopass.merge150.wgt10.zgt2.wig HMVEC_LLy-DS13185.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-LLy Blood vessel HMVEC-LLy NA "GSM736507,GSM736627" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_LLy-DS13185.twopass.merge150.wgt10.zgt2.wig HNPCEpiC-DS12467.twopass.merge150.wgt10.zgt2.wig UW DHS HNPCEpiC Epithelium HNPCEpiC NA "GSM736621,GSM736550" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HNPCEpiC-DS12467.twopass.merge150.wgt10.zgt2.wig HPAEC-DS12916.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS HPAEC Blood vessel HPAEC NA GSM1024763 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPAEC-DS12916.hg19.twopass.merge150.wgt10.zgt2.wig HPAF-DS13411.twopass.merge150.wgt10.zgt2.wig UW DHS HPAF Blood vessel HPAF NA "GSM736555,GSM736614" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPAF-DS13411.twopass.merge150.wgt10.zgt2.wig HPdLF-DS13573.twopass.merge150.wgt10.zgt2.wig UW DHS HPdLF Epithelium HPdLF NA "GSM736632,GSM736528" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPdLF-DS13573.twopass.merge150.wgt10.zgt2.wig HPF-DS13390.twopass.merge150.wgt10.zgt2.wig UW DHS HPF Lung HPF NA "GSM736574,GSM736503" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPF-DS13390.twopass.merge150.wgt10.zgt2.wig HRCE-DS10666.twopass.merge150.wgt10.zgt2.wig UW DHS HRCEpiC Epithelium HRCEpiC NA "GSM736549,GSM736557" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRCE-DS10666.twopass.merge150.wgt10.zgt2.wig HRE-DS10641.twopass.merge150.wgt10.zgt2.wig UW DHS HRE Epithelium HRE NA "GSM736527,GSM736548" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRE-DS10641.twopass.merge150.wgt10.zgt2.wig HRGEC-DS13716.twopass.merge150.wgt10.zgt2.wig UW DHS HRGEC Kidney HRGEC NA "GSM736499,GSM736618" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRGEC-DS13716.twopass.merge150.wgt10.zgt2.wig HRPEpiC-DS12583.twopass.merge150.wgt10.zgt2.wig UW DHS HRPEpiC Epithelium HRPEpiC NA "GSM736630,GSM736623" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRPEpiC-DS12583.twopass.merge150.wgt10.zgt2.wig HSMM-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HSMM Muscle HSMM NA "GSM816650,GSM736560,GSM736553" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HSMM-all.twopass.merge150.wgt10.zgt2.wig HSMM_D-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HSMM Muscle HSMM NA "GSM816650,GSM736560,GSM736553" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HSMM_D-all.twopass.merge150.wgt10.zgt2.wig hTH1-all.twopass.merge150.wgt10.zgt2.wig Combined DHS Th1 Blood Th1 NA "GSM736592,GSM1024760" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/hTH1-all.twopass.merge150.wgt10.zgt2.wig hTH2-DS7842.twopass.merge150.wgt10.zgt2.wig UW DHS Th2 Blood Th2 NA "GSM736502,GSM1024792" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/hTH2-DS7842.twopass.merge150.wgt10.zgt2.wig HUVEC-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HUVEC Blood vessel HUVEC NA "GSM816646,GSM736575,GSM736533" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HUVEC-all.twopass.merge150.wgt10.zgt2.wig HVMF-DS13981.twopass.merge150.wgt10.zgt2.wig UW DHS HVMF Connective HVMF NA "GSM736534,GSM736491" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HVMF-DS13981.twopass.merge150.wgt10.zgt2.wig Ishikawa_E_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS Ishikawa Uterus Ishikawa NA "GSM1008594,GSM1008593" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Ishikawa_E_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig Ishikawa_T_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS Ishikawa Uterus Ishikawa NA "GSM1008594,GSM1008593" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Ishikawa_T_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig Jurkat-DS12659.twopass.merge150.wgt10.zgt2.wig UW DHS Jurkat Blood Jurkat NA "GSM736501,GSM736492" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Jurkat-DS12659.twopass.merge150.wgt10.zgt2.wig K562-all.twopass.merge150.wgt10.zgt2.wig Combined DHS K562 Blood K562 NA "GSM816655,GSM1008602,GSM1008567,GSM1008601,GSM1008558,GSM1008580,GSM736629,GSM736566" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/K562-all.twopass.merge150.wgt10.zgt2.wig LNCap-all.twopass.merge150.wgt10.zgt2.wig Combined DHS LNCaP Prostate LNCaP NA "GSM816637,GSM816634,GSM736565,GSM736603" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/LNCap-all.twopass.merge150.wgt10.zgt2.wig MCF7-all.twopass.merge150.wgt10.zgt2.wig Combined DHS MCF-7 Breast MCF-7 NA "GSM816627,GSM1008581,GSM816670,GSM1008565,GSM1008603,GSM1024784,GSM1024783,GSM1024764,GSM1024767,GSM736581,GSM736588" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/MCF7-all.twopass.merge150.wgt10.zgt2.wig NB4-DS12543.twopass.merge150.wgt10.zgt2.wig UW DHS NB4 Blood NB4 NA "GSM736604,GSM736529" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NB4-DS12543.twopass.merge150.wgt10.zgt2.wig NHA-DS12800.twopass.merge150.wgt10.zgt2.wig UW DHS NH-A Nervous NH-A NA "GSM736544,GSM736584" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHA-DS12800.twopass.merge150.wgt10.zgt2.wig NHDF_Ad-DS12863.twopass.merge150.wgt10.zgt2.wig UW DHS NHDF-Ad Skin NHDF-Ad NA "GSM736567,GSM736520" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHDF_Ad-DS12863.twopass.merge150.wgt10.zgt2.wig NHDF_Neo-DS11923.twopass.merge150.wgt10.zgt2.wig UW DHS NHDF-neo Skin NHDF-neo NA "GSM736498,GSM736546" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHDF_Neo-DS11923.twopass.merge150.wgt10.zgt2.wig NHEK-all.twopass.merge150.wgt10.zgt2.wig Combined DHS NHEK Skin NHEK NA "GSM816635,GSM736545,GSM736556" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHEK-all.twopass.merge150.wgt10.zgt2.wig NHLF-DS12829.twopass.merge150.wgt10.zgt2.wig UW DHS NHLF Lung NHLF NA "GSM736612,GSM736536" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHLF-DS12829.twopass.merge150.wgt10.zgt2.wig NT2_D1-DS14575.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS NT2-D1 Testis NT2-D1 NA "GSM1024751,GSM1024795" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NT2_D1-DS14575.hg19.twopass.merge150.wgt10.zgt2.wig PANC1-DS9955.twopass.merge150.wgt10.zgt2.wig UW DHS PANC-1 Pancreas PANC-1 NA "GSM736517,GSM736519" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/PANC1-DS9955.twopass.merge150.wgt10.zgt2.wig PrEC-DS12098.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS PrEC Prostate PrEC NA "GSM1024742,GSM1024743" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/PrEC-DS12098.hg19.twopass.merge150.wgt10.zgt2.wig RPTEC-DS14061.twopass.merge150.wgt10.zgt2.wig UW DHS RPTEC Epithelium RPTEC NA "GSM736543,GSM736539" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/RPTEC-DS14061.twopass.merge150.wgt10.zgt2.wig RWPE_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS RWPE1 Prostate RWPE1 NA GSM1008595 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/RWPE_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig SAEC-DS10518.twopass.merge150.wgt10.zgt2.wig UW DHS SAEC Epithelium SAEC NA "GSM736608,GSM736617" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SAEC-DS10518.twopass.merge150.wgt10.zgt2.wig SkMC-DS11949.twopass.merge150.wgt10.zgt2.wig UW DHS SKMC Muscle SKMC NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SkMC-DS11949.twopass.merge150.wgt10.zgt2.wig SK_N_MC-DS14408.twopass.merge150.wgt10.zgt2.wig UW DHS SK-N-MC Brain SK-N-MC NA "GSM736522,GSM736570" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SK_N_MC-DS14408.twopass.merge150.wgt10.zgt2.wig SKNSH-DS8482.twopass.merge150.wgt10.zgt2.wig UW DHS SK-N-SH Brain SK-N-SH NA GSM1008585 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SKNSH-DS8482.twopass.merge150.wgt10.zgt2.wig WERI_Rb1-DS13681.twopass.merge150.wgt10.zgt2.wig UW DHS WERI-Rb-1 Eye WERI-Rb-1 NA "GSM736495,GSM736636" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/WERI_Rb1-DS13681.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnase8988tAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS 8988T Liver 8988T NA GSM816667 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnase8988tAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseAosmcSerumfreeAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS AoSMC Blood vessel AoSMC NA GSM816638 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseAosmcSerumfreeAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseChorionAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Chorion Fetal membrane Chorion NA GSM816628 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseChorionAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseCllAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS CLL Blood CLL NA GSM816664 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseCllAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseFibroblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Fibrobl Skin Fibrobl NA GSM816652 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseFibroblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseFibropAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS FibroP Skin FibroP NA GSM816626 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseFibropAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseGlioblaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Gliobla Brain Gliobla NA GSM816668 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGlioblaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseGm12891AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM12891 Blood GM12891 NA GSM816656 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm12891AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseGm12892AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM12892 Blood GM12892 NA GSM816657 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm12892AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseGm18507AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM18507 Blood GM18507 NA GSM816653 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm18507AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseGm19238AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM19238 Blood GM19238 NA GSM816658 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm19238AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseGm19239AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM19239 Blood GM19239 NA GSM816659 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm19239AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseGm19240AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM19240 Blood GM19240 NA GSM816648 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm19240AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseH9esAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS H9ES ES Cell H9ES NA GSM816629 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseH9esAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseHelas3Ifna4hAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS HeLa-S3 Cervix HeLa-S3 NA "GSM816633,GSM816643,GSM736564,GSM736510" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHelas3Ifna4hAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseHepatocytesAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Hepatocytes Liver Hepatocytes NA GSM816663 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHepatocytesAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseHpde6e6e7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS HPDE6-E6E7 Pancreatic duct HPDE6-E6E7 NA GSM816639 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHpde6e6e7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseHtr8AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS HTR8svn Blastula HTR8svn NA GSM816644 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHtr8AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseHuh75AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Huh-7.5 Liver Huh-7.5 NA GSM816671 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHuh75AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseHuh7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Huh-7 Liver Huh-7 NA GSM816641 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHuh7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseIpsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS iPS IPS iPS NA GSM816642 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseIpsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseLncapAndroAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS LNCaP Prostate LNCaP NA "GSM816637,GSM816634,GSM736565,GSM736603" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseLncapAndroAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseMcf7HypoxlacAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS MCF-7 Breast MCF-7 NA "GSM816627,GSM1008581,GSM816670,GSM1008565,GSM1008603,GSM1024784,GSM1024783,GSM1024764,GSM1024767,GSM736581,GSM736588" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMcf7HypoxlacAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseMedulloAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Medullo Brain Medullo NA GSM816636 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMedulloAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseMelanoAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Melano Skin Melano NA GSM816631 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMelanoAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseMyometrAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Myometr Myometrium Myometr NA GSM816630 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMyometrAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseOsteoblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Osteobl Bone Osteobl NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseOsteoblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnasePanisdAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS PanIsletD Pancreas PanIsletD NA GSM816666 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnasePanisdAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnasePanisletsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS PanIslets Pancreas PanIslets NA GSM816660 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnasePanisletsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnasePhteAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS pHTE Epithelium pHTE NA GSM816647 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnasePhteAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseProgfibAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS ProgFib Skin ProgFib NA GSM816661 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseProgfibAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseStellateAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Stellate Liver Stellate NA GSM816672 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseStellateAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseT47dAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS T-47D Breast T-47D NA "GSM816673,GSM1008576,GSM1024762,GSM1024761" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseT47dAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseUrotsaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Urothelia Urothelium Urothelia NA "GSM1008606,GSM1008605" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseUrotsaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig wgEncodeOpenChromDnaseUrotsaUt189AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Urothelia Urothelium Urothelia NA "GSM1008606,GSM1008605" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseUrotsaUt189AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig WI_38-DS14315.twopass.merge150.wgt10.zgt2.wig UW DHS WI-38 Embryonic lung WI-38 NA "GSM736613,GSM736526,GSM736613,GSM736526" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/WI_38-DS14315.twopass.merge150.wgt10.zgt2.wig WI_38_TAM-DS14323.twopass.merge150.wgt10.zgt2.wig UW DHS WI-38 Embryonic lung WI-38 NA "GSM736613,GSM736526,GSM736613,GSM736526" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/WI_38_TAM-DS14323.twopass.merge150.wgt10.zgt2.wig \ No newline at end of file +file lab datatype cell tissue shortcell individual acc url +A549-all.twopass.merge150.wgt10.zgt2.wig Combined DHS A549 Epithelium A549 NA "GSM816649,GSM736580,GSM736506" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/A549-all.twopass.merge150.wgt10.zgt2.wig +Adult_Th0_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS Adult_CD4+ Blood Adult_CD4+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Adult_Th0_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig +AG04449-DS12319.twopass.merge150.wgt10.zgt2.wig UW DHS AG04449 Skin AG04449 NA "GSM736562,GSM736590" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG04449-DS12319.twopass.merge150.wgt10.zgt2.wig +AG04450-DS12270.twopass.merge150.wgt10.zgt2.wig UW DHS AG04450 Lung AG04450 NA "GSM736514,GSM736563" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG04450-DS12270.twopass.merge150.wgt10.zgt2.wig +AG09309-DS12352.twopass.merge150.wgt10.zgt2.wig UW DHS AG09309 Skin AG09309 NA "GSM736551,GSM736616" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG09309-DS12352.twopass.merge150.wgt10.zgt2.wig +AG09319-DS12291.twopass.merge150.wgt10.zgt2.wig UW DHS AG09319 Gingival AG09319 NA "GSM736531,GSM736619" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG09319-DS12291.twopass.merge150.wgt10.zgt2.wig +AG10803-DS12384.twopass.merge150.wgt10.zgt2.wig UW DHS AG10803 Skin AG10803 NA "GSM736598,GSM736633" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AG10803-DS12384.twopass.merge150.wgt10.zgt2.wig +AoAF-DS13523.twopass.merge150.wgt10.zgt2.wig UW DHS AoAF Blood vessel AoAF NA "GSM736583,GSM736505" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/AoAF-DS13523.twopass.merge150.wgt10.zgt2.wig +BE_2_C-DS14625.twopass.merge150.wgt10.zgt2.wig UW DHS BE2_C Brain BE2_C NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/BE_2_C-DS14625.twopass.merge150.wgt10.zgt2.wig +BJ-DS10081.twopass.merge150.wgt10.zgt2.wig UW DHS BJ Skin BJ NA "GSM736518,GSM736596" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/BJ-DS10081.twopass.merge150.wgt10.zgt2.wig +CACO2-DS8235.twopass.merge150.wgt10.zgt2.wig UW DHS Caco-2 Colon Caco-2 NA "GSM736500,GSM736587" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CACO2-DS8235.twopass.merge150.wgt10.zgt2.wig +CD14-DS18065.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS CD14+ Blood CD14+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CD14-DS18065.hg19.twopass.merge150.wgt10.zgt2.wig +CD20-DS17541.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS CD20+ Blood CD20+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CD20-DS17541.hg19.twopass.merge150.wgt10.zgt2.wig +CD34-DS16814.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS CD34+ Blood CD34+ NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CD34-DS16814.hg19.twopass.merge150.wgt10.zgt2.wig +CMK-DS12393.twopass.merge150.wgt10.zgt2.wig UW DHS CMK Blood CMK NA GSM736607 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/CMK-DS12393.twopass.merge150.wgt10.zgt2.wig +E_myoblast_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS E_myoblast Muscle E_myoblast NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/E_myoblast_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig +GM06990-DS7748.twopass.merge150.wgt10.zgt2.wig UW DHS GM06990 Blood GM06990 NA "GSM736558,GSM736635" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM06990-DS7748.twopass.merge150.wgt10.zgt2.wig +GM12864-DS12431.twopass.merge150.wgt10.zgt2.wig UW DHS GM12864 Blood GM12864 NA GSM736525 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM12864-DS12431.twopass.merge150.wgt10.zgt2.wig +GM12865-DS12436.twopass.merge150.wgt10.zgt2.wig UW DHS GM12865 Blood GM12865 NA "GSM736512,GSM736561" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM12865-DS12436.twopass.merge150.wgt10.zgt2.wig +GM12878-all.twopass.merge150.wgt10.zgt2.wig Combined DHS GM12878 Blood GM12878 NA "GSM816665,GSM736496,GSM736620" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/GM12878-all.twopass.merge150.wgt10.zgt2.wig +HAc-DS14765.twopass.merge150.wgt10.zgt2.wig UW DHS HAc Cerebellar HAc NA "GSM736586,GSM736538" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAc-DS14765.twopass.merge150.wgt10.zgt2.wig +HAEpiC-DS12663.twopass.merge150.wgt10.zgt2.wig UW DHS HAEpiC Epithelium HAEpiC NA "GSM736631,GSM736606" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAEpiC-DS12663.twopass.merge150.wgt10.zgt2.wig +HAh-DS15192.twopass.merge150.wgt10.zgt2.wig UW DHS HA-h Brain hippocampus HA-h NA "GSM736594,GSM736535" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAh-DS15192.twopass.merge150.wgt10.zgt2.wig +HAsp-DS14790.twopass.merge150.wgt10.zgt2.wig UW DHS HA-sp Spinal cord HA-sp NA "GSM736537,GSM736625" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HAsp-DS14790.twopass.merge150.wgt10.zgt2.wig +HBMEC-DS13817.twopass.merge150.wgt10.zgt2.wig UW DHS HBMEC Blood vessel HBMEC NA "GSM736509,GSM736554" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HBMEC-DS13817.twopass.merge150.wgt10.zgt2.wig +HCFaa-DS13480.twopass.merge150.wgt10.zgt2.wig UW DHS HCFaa Heart HCFaa NA "GSM736494,GSM736601" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCFaa-DS13480.twopass.merge150.wgt10.zgt2.wig +HCF-DS12501.twopass.merge150.wgt10.zgt2.wig UW DHS HCF Heart HCF NA "GSM736568,GSM736540" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCF-DS12501.twopass.merge150.wgt10.zgt2.wig +HCM-DS12599.twopass.merge150.wgt10.zgt2.wig UW DHS HCM Heart HCM NA "GSM736516,GSM736504" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCM-DS12599.twopass.merge150.wgt10.zgt2.wig +HConF-DS11642.twopass.merge150.wgt10.zgt2.wig UW DHS HConF Eye HConF NA "GSM736547,GSM736515" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HConF-DS11642.twopass.merge150.wgt10.zgt2.wig +HCPEpiC-DS12447.twopass.merge150.wgt10.zgt2.wig UW DHS HCPEpiC Epithelium HCPEpiC NA "GSM736569,GSM736597" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCPEpiC-DS12447.twopass.merge150.wgt10.zgt2.wig +HCT116-DS13551.twopass.merge150.wgt10.zgt2.wig UW DHS HCT-116 Colon HCT-116 NA "GSM736600,GSM736493" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HCT116-DS13551.twopass.merge150.wgt10.zgt2.wig +HEEpiC-DS12763.twopass.merge150.wgt10.zgt2.wig UW DHS HEEpiC Epithelium HEEpiC NA "GSM736585,GSM736532" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HEEpiC-DS12763.twopass.merge150.wgt10.zgt2.wig +Hela-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HeLa-S3 Cervix HeLa-S3 NA "GSM816633,GSM816643,GSM736564,GSM736510" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Hela-all.twopass.merge150.wgt10.zgt2.wig +HepG2-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HepG2 Liver HepG2 NA "GSM816662,GSM736637,GSM736639" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HepG2-all.twopass.merge150.wgt10.zgt2.wig +HESC-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HESC ES Cell HESC NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HESC-all.twopass.merge150.wgt10.zgt2.wig +hESCT0-DS11909.twopass.merge150.wgt10.zgt2.wig UW DHS hESCT0 ES Cell hESCT0 NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/hESCT0-DS11909.twopass.merge150.wgt10.zgt2.wig +HFF-DS15115.twopass.merge150.wgt10.zgt2.wig UW DHS HFF Foreskin HFF NA "GSM736602,GSM736572" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HFF-DS15115.twopass.merge150.wgt10.zgt2.wig +HFF_MyC-DS15079.twopass.merge150.wgt10.zgt2.wig UW DHS HFF-Myc Foreskin HFF-Myc NA "GSM736524,GSM736605" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HFF_MyC-DS15079.twopass.merge150.wgt10.zgt2.wig +HGF-DS11752.twopass.merge150.wgt10.zgt2.wig UW DHS HGF Gingival HGF NA "GSM736579,GSM736576" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HGF-DS11752.twopass.merge150.wgt10.zgt2.wig +HIPEpiC-DS12684.twopass.merge150.wgt10.zgt2.wig UW DHS HIPEpiC Epithelium HIPEpiC NA "GSM736589,GSM736615" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HIPEpiC-DS12684.twopass.merge150.wgt10.zgt2.wig +HL60-DS11809.twopass.merge150.wgt10.zgt2.wig UW DHS HL-60 Blood HL-60 NA "GSM736626,GSM736595" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HL60-DS11809.twopass.merge150.wgt10.zgt2.wig +HMEC-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HMEC Breast HMEC NA "GSM816669,GSM736634,GSM736552" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMEC-all.twopass.merge150.wgt10.zgt2.wig +HMF-DS13363.twopass.merge150.wgt10.zgt2.wig UW DHS HMF Breast HMF NA "GSM736628,GSM736541" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMF-DS13363.twopass.merge150.wgt10.zgt2.wig +HMVEC_dAd-DS12957.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dAd Blood vessel HMVEC-dAd NA "GSM1024745,GSM1024747" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dAd-DS12957.hg19.twopass.merge150.wgt10.zgt2.wig +HMVEC_dBlAd-DS13337.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dBl-Ad Blood vessel HMVEC-dBl-Ad NA "GSM736609,GSM736523" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dBlAd-DS13337.twopass.merge150.wgt10.zgt2.wig +HMVEC_dBlNeo-DS13242.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dBl-Neo Blood vessel HMVEC-dBl-Neo NA "GSM736571,GSM736521" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dBlNeo-DS13242.twopass.merge150.wgt10.zgt2.wig +HMVEC_dLyAd-DS13261.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dLy-Ad Blood vessel HMVEC-dLy-Ad NA "GSM736599,GSM736591" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dLyAd-DS13261.twopass.merge150.wgt10.zgt2.wig +HMVEC_dLyNeo-DS13150.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dLy-Neo Blood vessel HMVEC-dLy-Neo NA "GSM736577,GSM736573" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dLyNeo-DS13150.twopass.merge150.wgt10.zgt2.wig +HMVEC_dNeo-DS12937.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-dNeo Blood vessel HMVEC-dNeo NA "GSM736611,GSM736624" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_dNeo-DS12937.twopass.merge150.wgt10.zgt2.wig +HMVEC_LBl-DS13372.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-LBl Blood vessel HMVEC-LBl NA "GSM736542,GSM736511" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_LBl-DS13372.twopass.merge150.wgt10.zgt2.wig +HMVEC_LLy-DS13185.twopass.merge150.wgt10.zgt2.wig UW DHS HMVEC-LLy Blood vessel HMVEC-LLy NA "GSM736507,GSM736627" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HMVEC_LLy-DS13185.twopass.merge150.wgt10.zgt2.wig +HNPCEpiC-DS12467.twopass.merge150.wgt10.zgt2.wig UW DHS HNPCEpiC Epithelium HNPCEpiC NA "GSM736621,GSM736550" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HNPCEpiC-DS12467.twopass.merge150.wgt10.zgt2.wig +HPAEC-DS12916.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS HPAEC Blood vessel HPAEC NA GSM1024763 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPAEC-DS12916.hg19.twopass.merge150.wgt10.zgt2.wig +HPAF-DS13411.twopass.merge150.wgt10.zgt2.wig UW DHS HPAF Blood vessel HPAF NA "GSM736555,GSM736614" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPAF-DS13411.twopass.merge150.wgt10.zgt2.wig +HPdLF-DS13573.twopass.merge150.wgt10.zgt2.wig UW DHS HPdLF Epithelium HPdLF NA "GSM736632,GSM736528" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPdLF-DS13573.twopass.merge150.wgt10.zgt2.wig +HPF-DS13390.twopass.merge150.wgt10.zgt2.wig UW DHS HPF Lung HPF NA "GSM736574,GSM736503" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HPF-DS13390.twopass.merge150.wgt10.zgt2.wig +HRCE-DS10666.twopass.merge150.wgt10.zgt2.wig UW DHS HRCEpiC Epithelium HRCEpiC NA "GSM736549,GSM736557" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRCE-DS10666.twopass.merge150.wgt10.zgt2.wig +HRE-DS10641.twopass.merge150.wgt10.zgt2.wig UW DHS HRE Epithelium HRE NA "GSM736527,GSM736548" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRE-DS10641.twopass.merge150.wgt10.zgt2.wig +HRGEC-DS13716.twopass.merge150.wgt10.zgt2.wig UW DHS HRGEC Kidney HRGEC NA "GSM736499,GSM736618" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRGEC-DS13716.twopass.merge150.wgt10.zgt2.wig +HRPEpiC-DS12583.twopass.merge150.wgt10.zgt2.wig UW DHS HRPEpiC Epithelium HRPEpiC NA "GSM736630,GSM736623" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HRPEpiC-DS12583.twopass.merge150.wgt10.zgt2.wig +HSMM-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HSMM Muscle HSMM NA "GSM816650,GSM736560,GSM736553" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HSMM-all.twopass.merge150.wgt10.zgt2.wig +HSMM_D-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HSMM Muscle HSMM NA "GSM816650,GSM736560,GSM736553" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HSMM_D-all.twopass.merge150.wgt10.zgt2.wig +hTH1-all.twopass.merge150.wgt10.zgt2.wig Combined DHS Th1 Blood Th1 NA "GSM736592,GSM1024760" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/hTH1-all.twopass.merge150.wgt10.zgt2.wig +hTH2-DS7842.twopass.merge150.wgt10.zgt2.wig UW DHS Th2 Blood Th2 NA "GSM736502,GSM1024792" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/hTH2-DS7842.twopass.merge150.wgt10.zgt2.wig +HUVEC-all.twopass.merge150.wgt10.zgt2.wig Combined DHS HUVEC Blood vessel HUVEC NA "GSM816646,GSM736575,GSM736533" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HUVEC-all.twopass.merge150.wgt10.zgt2.wig +HVMF-DS13981.twopass.merge150.wgt10.zgt2.wig UW DHS HVMF Connective HVMF NA "GSM736534,GSM736491" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/HVMF-DS13981.twopass.merge150.wgt10.zgt2.wig +Ishikawa_E_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS Ishikawa Uterus Ishikawa NA "GSM1008594,GSM1008593" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Ishikawa_E_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig +Ishikawa_T_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS Ishikawa Uterus Ishikawa NA "GSM1008594,GSM1008593" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Ishikawa_T_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig +Jurkat-DS12659.twopass.merge150.wgt10.zgt2.wig UW DHS Jurkat Blood Jurkat NA "GSM736501,GSM736492" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/Jurkat-DS12659.twopass.merge150.wgt10.zgt2.wig +K562-all.twopass.merge150.wgt10.zgt2.wig Combined DHS K562 Blood K562 NA "GSM816655,GSM1008602,GSM1008567,GSM1008601,GSM1008558,GSM1008580,GSM736629,GSM736566" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/K562-all.twopass.merge150.wgt10.zgt2.wig +LNCap-all.twopass.merge150.wgt10.zgt2.wig Combined DHS LNCaP Prostate LNCaP NA "GSM816637,GSM816634,GSM736565,GSM736603" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/LNCap-all.twopass.merge150.wgt10.zgt2.wig +MCF7-all.twopass.merge150.wgt10.zgt2.wig Combined DHS MCF-7 Breast MCF-7 NA "GSM816627,GSM1008581,GSM816670,GSM1008565,GSM1008603,GSM1024784,GSM1024783,GSM1024764,GSM1024767,GSM736581,GSM736588" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/MCF7-all.twopass.merge150.wgt10.zgt2.wig +NB4-DS12543.twopass.merge150.wgt10.zgt2.wig UW DHS NB4 Blood NB4 NA "GSM736604,GSM736529" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NB4-DS12543.twopass.merge150.wgt10.zgt2.wig +NHA-DS12800.twopass.merge150.wgt10.zgt2.wig UW DHS NH-A Nervous NH-A NA "GSM736544,GSM736584" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHA-DS12800.twopass.merge150.wgt10.zgt2.wig +NHDF_Ad-DS12863.twopass.merge150.wgt10.zgt2.wig UW DHS NHDF-Ad Skin NHDF-Ad NA "GSM736567,GSM736520" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHDF_Ad-DS12863.twopass.merge150.wgt10.zgt2.wig +NHDF_Neo-DS11923.twopass.merge150.wgt10.zgt2.wig UW DHS NHDF-neo Skin NHDF-neo NA "GSM736498,GSM736546" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHDF_Neo-DS11923.twopass.merge150.wgt10.zgt2.wig +NHEK-all.twopass.merge150.wgt10.zgt2.wig Combined DHS NHEK Skin NHEK NA "GSM816635,GSM736545,GSM736556" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHEK-all.twopass.merge150.wgt10.zgt2.wig +NHLF-DS12829.twopass.merge150.wgt10.zgt2.wig UW DHS NHLF Lung NHLF NA "GSM736612,GSM736536" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NHLF-DS12829.twopass.merge150.wgt10.zgt2.wig +NT2_D1-DS14575.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS NT2-D1 Testis NT2-D1 NA "GSM1024751,GSM1024795" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/NT2_D1-DS14575.hg19.twopass.merge150.wgt10.zgt2.wig +PANC1-DS9955.twopass.merge150.wgt10.zgt2.wig UW DHS PANC-1 Pancreas PANC-1 NA "GSM736517,GSM736519" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/PANC1-DS9955.twopass.merge150.wgt10.zgt2.wig +PrEC-DS12098.hg19.twopass.merge150.wgt10.zgt2.wig UW DHS PrEC Prostate PrEC NA "GSM1024742,GSM1024743" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/PrEC-DS12098.hg19.twopass.merge150.wgt10.zgt2.wig +RPTEC-DS14061.twopass.merge150.wgt10.zgt2.wig UW DHS RPTEC Epithelium RPTEC NA "GSM736543,GSM736539" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/RPTEC-DS14061.twopass.merge150.wgt10.zgt2.wig +RWPE_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig UW DHS RWPE1 Prostate RWPE1 NA GSM1008595 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/RWPE_AllReps.30000000.twopass.merge150.wgt10.zgt2.wig +SAEC-DS10518.twopass.merge150.wgt10.zgt2.wig UW DHS SAEC Epithelium SAEC NA "GSM736608,GSM736617" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SAEC-DS10518.twopass.merge150.wgt10.zgt2.wig +SkMC-DS11949.twopass.merge150.wgt10.zgt2.wig UW DHS SKMC Muscle SKMC NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SkMC-DS11949.twopass.merge150.wgt10.zgt2.wig +SK_N_MC-DS14408.twopass.merge150.wgt10.zgt2.wig UW DHS SK-N-MC Brain SK-N-MC NA "GSM736522,GSM736570" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SK_N_MC-DS14408.twopass.merge150.wgt10.zgt2.wig +SKNSH-DS8482.twopass.merge150.wgt10.zgt2.wig UW DHS SK-N-SH Brain SK-N-SH NA GSM1008585 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/SKNSH-DS8482.twopass.merge150.wgt10.zgt2.wig +WERI_Rb1-DS13681.twopass.merge150.wgt10.zgt2.wig UW DHS WERI-Rb-1 Eye WERI-Rb-1 NA "GSM736495,GSM736636" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/WERI_Rb1-DS13681.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnase8988tAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS 8988T Liver 8988T NA GSM816667 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnase8988tAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseAosmcSerumfreeAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS AoSMC Blood vessel AoSMC NA GSM816638 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseAosmcSerumfreeAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseChorionAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Chorion Fetal membrane Chorion NA GSM816628 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseChorionAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseCllAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS CLL Blood CLL NA GSM816664 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseCllAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseFibroblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Fibrobl Skin Fibrobl NA GSM816652 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseFibroblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseFibropAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS FibroP Skin FibroP NA GSM816626 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseFibropAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseGlioblaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Gliobla Brain Gliobla NA GSM816668 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGlioblaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseGm12891AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM12891 Blood GM12891 NA GSM816656 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm12891AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseGm12892AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM12892 Blood GM12892 NA GSM816657 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm12892AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseGm18507AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM18507 Blood GM18507 NA GSM816653 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm18507AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseGm19238AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM19238 Blood GM19238 NA GSM816658 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm19238AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseGm19239AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM19239 Blood GM19239 NA GSM816659 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm19239AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseGm19240AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS GM19240 Blood GM19240 NA GSM816648 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseGm19240AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseH9esAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS H9ES ES Cell H9ES NA GSM816629 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseH9esAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseHelas3Ifna4hAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS HeLa-S3 Cervix HeLa-S3 NA "GSM816633,GSM816643,GSM736564,GSM736510" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHelas3Ifna4hAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseHepatocytesAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Hepatocytes Liver Hepatocytes NA GSM816663 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHepatocytesAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseHpde6e6e7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS HPDE6-E6E7 Pancreatic duct HPDE6-E6E7 NA GSM816639 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHpde6e6e7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseHtr8AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS HTR8svn Blastula HTR8svn NA GSM816644 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHtr8AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseHuh75AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Huh-7.5 Liver Huh-7.5 NA GSM816671 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHuh75AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseHuh7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Huh-7 Liver Huh-7 NA GSM816641 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseHuh7AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseIpsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS iPS IPS iPS NA GSM816642 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseIpsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseLncapAndroAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS LNCaP Prostate LNCaP NA "GSM816637,GSM816634,GSM736565,GSM736603" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseLncapAndroAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseMcf7HypoxlacAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS MCF-7 Breast MCF-7 NA "GSM816627,GSM1008581,GSM816670,GSM1008565,GSM1008603,GSM1024784,GSM1024783,GSM1024764,GSM1024767,GSM736581,GSM736588" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMcf7HypoxlacAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseMedulloAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Medullo Brain Medullo NA GSM816636 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMedulloAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseMelanoAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Melano Skin Melano NA GSM816631 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMelanoAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseMyometrAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Myometr Myometrium Myometr NA GSM816630 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseMyometrAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseOsteoblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Osteobl Bone Osteobl NA Lookup ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseOsteoblAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnasePanisdAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS PanIsletD Pancreas PanIsletD NA GSM816666 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnasePanisdAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnasePanisletsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS PanIslets Pancreas PanIslets NA GSM816660 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnasePanisletsAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnasePhteAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS pHTE Epithelium pHTE NA GSM816647 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnasePhteAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseProgfibAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS ProgFib Skin ProgFib NA GSM816661 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseProgfibAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseStellateAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Stellate Liver Stellate NA GSM816672 ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseStellateAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseT47dAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS T-47D Breast T-47D NA "GSM816673,GSM1008576,GSM1024762,GSM1024761" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseT47dAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseUrotsaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Urothelia Urothelium Urothelia NA "GSM1008606,GSM1008605" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseUrotsaAlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +wgEncodeOpenChromDnaseUrotsaUt189AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig Duke:UNC:UTA DHS Urothelia Urothelium Urothelia NA "GSM1008606,GSM1008605" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/wgEncodeOpenChromDnaseUrotsaUt189AlnAllReps.30000000.twopass.merge150.wgt10.zgt2.wig +WI_38-DS14315.twopass.merge150.wgt10.zgt2.wig UW DHS WI-38 Embryonic lung WI-38 NA "GSM736613,GSM736526,GSM736613,GSM736526" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/WI_38-DS14315.twopass.merge150.wgt10.zgt2.wig +WI_38_TAM-DS14323.twopass.merge150.wgt10.zgt2.wig UW DHS WI-38 Embryonic lung WI-38 NA "GSM736613,GSM736526,GSM736613,GSM736526" ftp://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/openchrom/jan2011/combined_hotspots/WI_38_TAM-DS14323.twopass.merge150.wgt10.zgt2.wig \ No newline at end of file From 63b8ba9639f03428b80b41f041ddcad1ea811e14 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Wed, 30 Sep 2015 22:29:13 +0100 Subject: [PATCH 12/26] Fix DOCUMENT_ROOT for v1.1 --- webserver/cgi-bin/index.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/webserver/cgi-bin/index.pl b/webserver/cgi-bin/index.pl index c19de77..e078801 100755 --- a/webserver/cgi-bin/index.pl +++ b/webserver/cgi-bin/index.pl @@ -25,7 +25,7 @@ ## # The location of the HTML pages for this server on the filesystem -my $DOCUMENT_ROOT = "/var/www/eFORGE/html"; +my $DOCUMENT_ROOT = "/var/www/eFORGE.v1.1/html"; # The base URL (without the server name) for this server. For instance: # Running on http://server.org/ -> $WEB_ROOT = "" From 1f2812f69cc8c230ceb47e4b80b851d7756c89e7 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Mon, 25 Jan 2016 16:35:38 +0000 Subject: [PATCH 13/26] Fix buglet: PDF was always showing default thresholds in the legend --- eForge/ePlot.pm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/eForge/ePlot.pm b/eForge/ePlot.pm index be0236a..07f0b04 100644 --- a/eForge/ePlot.pm +++ b/eForge/ePlot.pm @@ -131,11 +131,11 @@ mtext(2, text='-log10 binomial p-value', line=2, cex=1.4) # Add legend (internal color first) palette(c('white', '$msig', '$sig')) -legend('topleft', pch=19, legend=c('q < 0.01', 'q < 0.05', 'non-sig'), col = 3:1, cex=0.8, inset=c(0.001, 0.005), box.col='white', title='FDR q-value', text.col='white', bg='white') +legend('topleft', pch=19, legend=c('q < $t2', 'q < $t1', 'non-sig'), col = 3:1, cex=0.8, inset=c(0.001, 0.005), box.col='white', title='FDR q-value', text.col='white', bg='white') # Add contour to the points in the legend palette(c('$ns', '$msig', 'black')) -legend('topleft', pch=1, legend=c('q < 0.01', 'q < 0.05', 'non-sig'), col = 3:1, cex=0.8, inset=c(0.001, 0.005), box.col='darkgrey', title='FDR q-value') +legend('topleft', pch=1, legend=c('q < $t2', 'q < $t1', 'non-sig'), col = 3:1, cex=0.8, inset=c(0.001, 0.005), box.col='darkgrey', title='FDR q-value') palette('default') dev.off() From b1dce9603deddeaa0db2c4867e5a3788b52d6ef0 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Mon, 25 Jan 2016 17:31:24 +0000 Subject: [PATCH 14/26] Fix mixup between strict and marginal thresholds of significance. Also fixes pink color on dChart --- eForge/ePlot.pm | 33 ++++++++++++++++++--------------- eforge.pl | 19 +++++++++++-------- webserver/cgi-bin/index.pl | 37 ++++++++++++++++++------------------- 3 files changed, 47 insertions(+), 42 deletions(-) diff --git a/eForge/ePlot.pm b/eForge/ePlot.pm index 07f0b04..602ff65 100644 --- a/eForge/ePlot.pm +++ b/eForge/ePlot.pm @@ -71,7 +71,7 @@ This is the original code using standard R plot to generate a static pdf. sub Chart{ print "Making static chart.\n"; - my ($filename, $lab, $resultsdir, $tissues, $cells, $label, $t1, $t2, $data) = @_; + my ($filename, $lab, $resultsdir, $tissues, $cells, $label, $t_marginal, $t_strict, $data) = @_; my $Rdir = $resultsdir; my $chart = "$lab.chart.pdf"; my $rfile = "$Rdir/$lab.chart.R"; @@ -80,17 +80,17 @@ sub Chart{ open my $rfh, ">", $rfile; -#results\$Class<-cut(results\$Pvalue, breaks =c(min(results\$Pvalue), $t1, $t2, max(results\$Pvalue)), labels=FALSE, include.lowest=TRUE) # 99 and 95% CIs 1, 2, 3 -$t1 = sprintf("%.2f", $t1); -$t2 = sprintf("%.2f", $t2); +#results\$Class<-cut(results\$Pvalue, breaks =c(min(results\$Pvalue), $t_marginal, $t_strict, max(results\$Pvalue)), labels=FALSE, include.lowest=TRUE) # 99 and 95% CIs 1, 2, 3 +$t_marginal = sprintf("%.2f", $t_marginal); +$t_strict = sprintf("%.2f", $t_strict); print $rfh "setwd('$Rdir') results<-read.table('$filename', header=TRUE,sep='\\t') -# Class splits the data into non-significant, marginally significant and significant according to $t1 and $t2 (in -log10 scale) -results\$Class <- cut(results\$Pvalue, breaks =c(0, $t2, $t1, 1)/length(unique(results[,'Tissue'])), labels=FALSE, include.lowest=TRUE) +# Class splits the data into non-significant, marginally significant and significant according to $t_marginal and $t_strict (in -log10 scale) +results\$Class <- cut(results\$Pvalue, breaks =c(0, $t_strict, $t_marginal, 1)/length(unique(results[,'Tissue'])), labels=FALSE, include.lowest=TRUE) # Class splits the data into non-significant, marginally significant and significant according to q-value (B-Y FDR adjusted) -results\$Class2 <- cut(results\$Qvalue, breaks =c(0, $t2, $t1, 1), labels=FALSE, include.lowest=TRUE) +results\$Class2 <- cut(results\$Qvalue, breaks =c(0, $t_strict, $t_marginal, 1), labels=FALSE, include.lowest=TRUE) # Re-order the entries according to tissue first and then cell type/line tissue.cell.order <- unique(results[, c('Tissue', 'Cell')]) @@ -131,11 +131,11 @@ mtext(2, text='-log10 binomial p-value', line=2, cex=1.4) # Add legend (internal color first) palette(c('white', '$msig', '$sig')) -legend('topleft', pch=19, legend=c('q < $t2', 'q < $t1', 'non-sig'), col = 3:1, cex=0.8, inset=c(0.001, 0.005), box.col='white', title='FDR q-value', text.col='white', bg='white') +legend('topleft', pch=19, legend=c('q < $t_strict', 'q < $t_marginal', 'non-sig'), col = 3:1, cex=0.8, inset=c(0.001, 0.005), box.col='white', title='FDR q-value', text.col='white', bg='white') # Add contour to the points in the legend palette(c('$ns', '$msig', 'black')) -legend('topleft', pch=1, legend=c('q < $t2', 'q < $t1', 'non-sig'), col = 3:1, cex=0.8, inset=c(0.001, 0.005), box.col='darkgrey', title='FDR q-value') +legend('topleft', pch=1, legend=c('q < $t_strict', 'q < $t_marginal', 'non-sig'), col = 3:1, cex=0.8, inset=c(0.001, 0.005), box.col='darkgrey', title='FDR q-value') palette('default') dev.off() @@ -153,7 +153,7 @@ Make dimple interactive chart. =cut sub dChart{ - my ($filename, $lab, $resultsdir, $data, $label, $t1, $t2, $web) = @_; + my ($filename, $lab, $resultsdir, $data, $label, $t_marginal, $t_strict, $web) = @_; print "Making dChart.\n"; my $chart = "$lab.dchart.html"; @@ -163,19 +163,22 @@ sub dChart{ print $rcfh "setwd(\"$Rdir\") results<-read.table(\"$filename\", header = TRUE, sep=\"\\t\") -# Class splits the data into non-significant, marginally significant and significant according to $t1 and $t2 (in -log10 scale) -results\$Class <- cut(results\$Pvalue, breaks =c(0, $t2, $t1, 1)/length(unique(results[,'Tissue'])), labels=FALSE, include.lowest=TRUE) +# Class splits the data into non-significant, marginally significant and significant according to $t_marginal and $t_strict (in -log10 scale) +results\$Class <- cut(results\$Pvalue, breaks =c(0, $t_strict, $t_marginal, 1)/length(unique(results[,'Tissue'])), labels=FALSE, include.lowest=TRUE) # Class splits the data into non-significant, marginally significant and significant according to q-value (B-Y FDR adjusted) -results\$Class2 <- cut(results\$Qvalue, breaks =c(0, $t2, $t1, 1), labels=FALSE, include.lowest=TRUE) +results\$Class2 <- cut(results\$Qvalue, breaks =c(0, $t_strict, $t_marginal, 1), labels=FALSE, include.lowest=TRUE) color.axis.palette = c(); if (length(which(results\$Class2 == 1)) > 0 ) { color.axis.palette = c('red'); } if (length(which(results\$Class2 == 2)) > 0 ) { - color.axis.palette = c(color.axis.palette, 'pink'); + color.axis.palette = c(color.axis.palette, '#FF82ab'); +} +color.axis.palette = c(color.axis.palette, 'lightblue'); +if (length(color.axis.palette) < 2) { + color.axis.palette = c(color.axis.palette, 'lightblue'); # Add it twice to force the color if only non-significant values } -color.axis.palette = c(color.axis.palette, 'lightblue', 'lightblue'); # Add it twice to force the color if only non-significant values results\$log10pvalue <- -log10(results\$Pvalue) diff --git a/eforge.pl b/eforge.pl index 1a53a9c..de3c034 100644 --- a/eforge.pl +++ b/eforge.pl @@ -338,15 +338,18 @@ =head1 ACKNOWLEDGEMENTS # Define the thresholds to use. -my ($t1, $t2); +my ($t_marginal, $t_strict); if (defined $thresh) { - ($t1, $t2) = split(",", $thresh); - unless (looks_like_number($t1) && looks_like_number($t2)){ - die "You must specify numerical p value thresholds in a comma separated list"; + ($t_marginal, $t_strict) = split(",", $thresh); + unless (looks_like_number($t_marginal) && looks_like_number($t_strict)){ + die "You must specify numerical p value thresholds in a comma separated list\n"; + } + unless ((1 >= $t_marginal) && ($t_marginal >= $t_strict) && ($t_strict >= 0)) { + die "The p-value thresholds should be 1 >= T.marginal >= T.strict >= 0\n"; } } else { - $t1 = 0.05; # set binomial p values, bonferroni is applied later based on number of samples (cells) - $t2 = 0.01; + $t_marginal = 0.05; # set binomial p values, bonferroni is applied later based on number of samples (cells) + $t_strict = 0.01; } # mvps need to come either from a file or a list @@ -576,8 +579,8 @@ =head1 ACKNOWLEDGEMENTS warn "[".scalar(localtime())."] Generating plots...\n"; unless (defined $noplot){ #Plotting and table routines - Chart($filename, $lab, $out_dir, $tissues, $cells, $label, $t1, $t2, $data); # basic pdf plot - dChart($filename, $lab, $out_dir, $data, $label, $t1, $t2, $web); # rCharts Dimple chart + Chart($filename, $lab, $out_dir, $tissues, $cells, $label, $t_marginal, $t_strict, $data); # basic pdf plot + dChart($filename, $lab, $out_dir, $data, $label, $t_marginal, $t_strict, $web); # rCharts Dimple chart table($filename, $lab, $out_dir, $web); # Datatables chart } diff --git a/webserver/cgi-bin/index.pl b/webserver/cgi-bin/index.pl index e078801..2f32255 100755 --- a/webserver/cgi-bin/index.pl +++ b/webserver/cgi-bin/index.pl @@ -277,10 +277,10 @@ sub print_form { textfield('reps', '1000', 10)]), td(["Significance threshold:", ""]), - td(["      Min:", - textfield('thresh1', '0.01', 10)]), - td(["      Max:", - textfield('thresh2', '0.05', 10)]), + td(["      Strict:", + textfield('thresh_strict', '0.01', 10)]), + td(["      Marginal:", + textfield('thresh_marginal', '0.05', 10)]), th({-colspan=>2}, ["<hr>"]), @@ -393,27 +393,26 @@ sub validate_form { } push(@$validated_args, "--reps", $reps); - my $thresh1 = param("thresh1"); - if (!$thresh1 or $thresh1 !~ /^\d+(\.\d*)?$/) { - push(@error_messages, "Min. significance threshold must be a positive number."); - } elsif ($thresh1 >= 1) { - push(@error_messages, "Min. significance threshold must be less than 1."); + my $thresh_strict = param("thresh_strict"); + if (!$thresh_strict or $thresh_strict !~ /^\d+(\.\d*)?$/) { + push(@error_messages, "Strict significance threshold must be a positive number."); + } elsif ($thresh_strict >= 1) { + push(@error_messages, "Strict significance threshold must be less than 1."); } - my $thresh2 = param("thresh2"); - if (!$thresh2 or $thresh2 !~ /^\d+(\.\d*)?$/) { - push(@error_messages, "Max. significance threshold must be a positive number."); - } elsif ($thresh2 >= 1) { - push(@error_messages, "Max. significance threshold must be less than 1."); + my $thresh_marginal = param("thresh_marginal"); + if (!$thresh_marginal or $thresh_marginal !~ /^\d+(\.\d*)?$/) { + push(@error_messages, "Marginal significance threshold must be a positive number."); + } elsif ($thresh_marginal >= 1) { + push(@error_messages, "Marginal significance threshold must be less than 1."); } - if ($thresh1 > $thresh2) { + if ($thresh_strict > $thresh_marginal) { print $q->header; - push(@error_messages, "Min. significance threshold must be less than max. significance". - " threshold."); + push(@error_messages, "Strict significance threshold must be less than marginal one."); return 0; } - push(@$validated_args, "--thresh", "$thresh1,$thresh2"); + push(@$validated_args, "--thresh", "$thresh_marginal,$thresh_strict"); if (@error_messages) { print $q->header; @@ -915,7 +914,7 @@ sub print_help_page { <br \>", "<strong>Significance threshold</strong><br \><br \> - Alter the default binomial p value thresholds. (0 < Min < Max < 1) + Alter the default binomial p value thresholds. (0 < Strict < Marginal < 1) <br \>", ); From a84698906849c6275ff4d0ed2f94afda76a3c9ae Mon Sep 17 00:00:00 2001 From: charlesbreeze <charlesbreeze@users.noreply.github.com> Date: Wed, 6 Apr 2016 15:05:06 +0100 Subject: [PATCH 15/26] Added files via upload added blueprint decode file --- database/blueprint.decode | 1 + 1 file changed, 1 insertion(+) create mode 100644 database/blueprint.decode diff --git a/database/blueprint.decode b/database/blueprint.decode new file mode 100644 index 0000000..cc1e9d2 --- /dev/null +++ b/database/blueprint.decode @@ -0,0 +1 @@ +BP_DG-75_d01.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA Sporadic_Burkitt_lymphoma Cell Line Hotspots DG-75_Sporadic_Burkitt_lymphoma NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/DG-75/Sporadic_Burkitt_lymphoma/DNase-Hypersensitivity/NCMLS S00C0J41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_B-glucan Venous Blood Hotspots macrophage_-_T_6days_B-glucan Female_30_35_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031319896021/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS BP_U-266_d01.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA Multiple_myeloma Cell Line Hotspots U-266_Multiple_myeloma NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/U-266/Multiple_myeloma/DNase-Hypersensitivity/NCMLS S00CR241.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_untreated Venous Blood Hotspots macrophage_-_T_6days_untreated Male_55_60_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031318490130/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS BP_Z-138_d01.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA Mantle_cell_lymphoma Cell Line Hotspots Z-138_Mantle_cell_lymphoma NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/Z-138/Mantle_cell_lymphoma/DNase-Hypersensitivity/NCMLS S00CS041.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_LPS Venous Blood Hotspots macrophage_-_T_6days_LPS Male_55_60_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031318490130/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS C0010K46.DNase.hotspot_v3.20130415.bed NCMLS DNase-seq NA CD14-positive_CD16-negative_classical_monocyte Venous Blood Hotspots CD14-positive_CD16-negative_classical_monocyte Female_60_65_years ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C0010K/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS S00CTZ41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_B-glucan Venous Blood Hotspots macrophage_-_T_6days_B-glucan Male_55_60_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031318490130/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS C0011I43.DNase.hotspot_v3.20130415.bed NCMLS DNase-seq NA CD14-positive_CD16-negative_classical_monocyte Venous Blood Hotspots CD14-positive_CD16-negative_classical_monocyte Female_50_55_years ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C0011I/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS S00EPZ41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA monocyte_-_T_0days Venous Blood Hotspots monocyte_-_T_0days Male_55_60_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031324825721/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS C001UY46.DNase.hotspot_v3.20130415.bed NCMLS DNase-seq NA CD14-positive_CD16-negative_classical_monocyte Venous Blood Hotspots CD14-positive_CD16-negative_classical_monocyte Male_60_65_years ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C001UY/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS S00HRJ41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_untreated Venous Blood Hotspots macrophage_-_T_6days_untreated Male_55_60_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406635321/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS C004084E.DNase.hotspot_v3.20130415.bed NCMLS DNase-seq NA CD14-positive_CD16-negative_classical_monocyte Venous Blood Hotspots CD14-positive_CD16-negative_classical_monocyte Male_55_60_years ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C00408/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS S00HSH41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_LPS Venous Blood Hotspots macrophage_-_T_6days_LPS Male_55_60_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406635321/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS C005PS4E.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA CD14_positive_CD16_negative_classical_monocyte Cord Blood Hotspots CD14_positive_CD16_negative_classical_monocyte Female ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cord_blood/C005PS/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS S00HTF41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_B-glucan Venous Blood Hotspots macrophage_-_T_6days_B-glucan Male_55_60_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406635321/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS C005VG45.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA macrophage Venous Blood Hotspots macrophage Male_60_65_years ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C005VG/macrophage/DNase-Hypersensitivity/NCMLS S00JPF41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA monocyte_-_T_0days Venous Blood Hotspots monocyte_-_T_0days Female_45_50_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406634921/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS C006NS47.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell Cord Blood Hotspots CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell Male ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cord_blood/C006NS/CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell/DNase-Hypersensitivity/NCMLS S00JQD41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_untreated Venous Blood Hotspots macrophage_-_T_6days_untreated Female_45_50_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406634921/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS C006UE47.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA macrophage Venous Blood Hotspots macrophage Male_65_70_years ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C006UE/macrophage/DNase-Hypersensitivity/NCMLS S00JRB41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_LPS Venous Blood Hotspots macrophage_-_T_6days_LPS Female_45_50_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406634921/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS S001MJ48.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA inflammatory_macrophage Venous Blood Hotspots inflammatory_macrophage Male_55_60_years ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS S00JS941.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_B-glucan Venous Blood Hotspots macrophage_-_T_6days_B-glucan Female_45_50_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406634921/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS S001MJ4A.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA inflammatory_macrophage Venous Blood Hotspots inflammatory_macrophage Male_55_60_years ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS bp_KARPAS-422_d01.DNase.hotspot_v3.20131126.bed NCMLS DNase-seq NA Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma Cell Line Hotspots KARPAS-422_Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/KARPAS-422/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS S005FH41.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA Acute_myeloid_leukemia Bone Marrow Hotspots Acute_myeloid_leukemia Female_70_75_years_Acute_Myeloid_leukaemia ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Bone_marrow/UMCG_2012-082/Acute_myeloid_leukemia/DNase-Hypersensitivity/NCMLS bp_SU-DHL-5_d01.DNase.hotspot_v3.20131126.bed NCMLS DNase-seq NA Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma Cell Line Hotspots SU-DHL-5_Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/SU-DHL-5/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS S00BXV41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_untreated Venous Blood Hotspots macrophage_-_T_6days_untreated Female_30_35_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031319896021/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS S00BYT41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_LPS Venous Blood Hotspots macrophage_-_T_6days_LPS Female_30_35_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031319896021/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS \ No newline at end of file From e982d87cc04da46b984414b759d2bc01db307aaa Mon Sep 17 00:00:00 2001 From: charlesbreeze <charlesbreeze@users.noreply.github.com> Date: Thu, 7 Apr 2016 16:27:30 +0100 Subject: [PATCH 16/26] Update blueprint.decode --- database/blueprint.decode | 32 +++++++++++++++++++++++++++++++- 1 file changed, 31 insertions(+), 1 deletion(-) diff --git a/database/blueprint.decode b/database/blueprint.decode index cc1e9d2..f498876 100644 --- a/database/blueprint.decode +++ b/database/blueprint.decode @@ -1 +1,31 @@ -BP_DG-75_d01.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA Sporadic_Burkitt_lymphoma Cell Line Hotspots DG-75_Sporadic_Burkitt_lymphoma NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/DG-75/Sporadic_Burkitt_lymphoma/DNase-Hypersensitivity/NCMLS S00C0J41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_B-glucan Venous Blood Hotspots macrophage_-_T_6days_B-glucan Female_30_35_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031319896021/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS BP_U-266_d01.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA Multiple_myeloma Cell Line Hotspots U-266_Multiple_myeloma NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/U-266/Multiple_myeloma/DNase-Hypersensitivity/NCMLS S00CR241.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_untreated Venous Blood Hotspots macrophage_-_T_6days_untreated Male_55_60_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031318490130/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS BP_Z-138_d01.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA Mantle_cell_lymphoma Cell Line Hotspots Z-138_Mantle_cell_lymphoma NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/Z-138/Mantle_cell_lymphoma/DNase-Hypersensitivity/NCMLS S00CS041.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_LPS Venous Blood Hotspots macrophage_-_T_6days_LPS Male_55_60_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031318490130/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS C0010K46.DNase.hotspot_v3.20130415.bed NCMLS DNase-seq NA CD14-positive_CD16-negative_classical_monocyte Venous Blood Hotspots CD14-positive_CD16-negative_classical_monocyte Female_60_65_years ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C0010K/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS S00CTZ41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_B-glucan Venous Blood Hotspots macrophage_-_T_6days_B-glucan Male_55_60_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031318490130/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS C0011I43.DNase.hotspot_v3.20130415.bed NCMLS DNase-seq NA CD14-positive_CD16-negative_classical_monocyte Venous Blood Hotspots CD14-positive_CD16-negative_classical_monocyte Female_50_55_years ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C0011I/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS S00EPZ41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA monocyte_-_T_0days Venous Blood Hotspots monocyte_-_T_0days Male_55_60_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031324825721/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS C001UY46.DNase.hotspot_v3.20130415.bed NCMLS DNase-seq NA CD14-positive_CD16-negative_classical_monocyte Venous Blood Hotspots CD14-positive_CD16-negative_classical_monocyte Male_60_65_years ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C001UY/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS S00HRJ41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_untreated Venous Blood Hotspots macrophage_-_T_6days_untreated Male_55_60_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406635321/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS C004084E.DNase.hotspot_v3.20130415.bed NCMLS DNase-seq NA CD14-positive_CD16-negative_classical_monocyte Venous Blood Hotspots CD14-positive_CD16-negative_classical_monocyte Male_55_60_years ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C00408/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS S00HSH41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_LPS Venous Blood Hotspots macrophage_-_T_6days_LPS Male_55_60_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406635321/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS C005PS4E.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA CD14_positive_CD16_negative_classical_monocyte Cord Blood Hotspots CD14_positive_CD16_negative_classical_monocyte Female ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cord_blood/C005PS/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS S00HTF41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_B-glucan Venous Blood Hotspots macrophage_-_T_6days_B-glucan Male_55_60_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406635321/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS C005VG45.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA macrophage Venous Blood Hotspots macrophage Male_60_65_years ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C005VG/macrophage/DNase-Hypersensitivity/NCMLS S00JPF41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA monocyte_-_T_0days Venous Blood Hotspots monocyte_-_T_0days Female_45_50_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406634921/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS C006NS47.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell Cord Blood Hotspots CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell Male ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cord_blood/C006NS/CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell/DNase-Hypersensitivity/NCMLS S00JQD41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_untreated Venous Blood Hotspots macrophage_-_T_6days_untreated Female_45_50_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406634921/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS C006UE47.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA macrophage Venous Blood Hotspots macrophage Male_65_70_years ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C006UE/macrophage/DNase-Hypersensitivity/NCMLS S00JRB41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_LPS Venous Blood Hotspots macrophage_-_T_6days_LPS Female_45_50_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406634921/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS S001MJ48.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA inflammatory_macrophage Venous Blood Hotspots inflammatory_macrophage Male_55_60_years ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS S00JS941.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_B-glucan Venous Blood Hotspots macrophage_-_T_6days_B-glucan Female_45_50_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406634921/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS S001MJ4A.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA inflammatory_macrophage Venous Blood Hotspots inflammatory_macrophage Male_55_60_years ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS bp_KARPAS-422_d01.DNase.hotspot_v3.20131126.bed NCMLS DNase-seq NA Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma Cell Line Hotspots KARPAS-422_Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/KARPAS-422/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS S005FH41.DNase.hotspot_v3.20130819.bed NCMLS DNase-seq NA Acute_myeloid_leukemia Bone Marrow Hotspots Acute_myeloid_leukemia Female_70_75_years_Acute_Myeloid_leukaemia ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Bone_marrow/UMCG_2012-082/Acute_myeloid_leukemia/DNase-Hypersensitivity/NCMLS bp_SU-DHL-5_d01.DNase.hotspot_v3.20131126.bed NCMLS DNase-seq NA Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma Cell Line Hotspots SU-DHL-5_Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/SU-DHL-5/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS S00BXV41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_untreated Venous Blood Hotspots macrophage_-_T_6days_untreated Female_30_35_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031319896021/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS S00BYT41.DNase.hotspot_v3.20141014.bed NCMLS DNase-seq NA macrophage_-_T_6days_LPS Venous Blood Hotspots macrophage_-_T_6days_LPS Female_30_35_years_Healthy ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031319896021/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS \ No newline at end of file +file lab datatype cell tissue shortcell individual acc url +BP_DG-75_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Sporadic_Burkitt_lymphoma Cell Line DG-75_Sporadic_Burkitt_lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/DG-75/Sporadic_Burkitt_lymphoma/DNase-Hypersensitivity/NCMLS +S00C0J41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031319896021/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS +BP_U-266_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Multiple_myeloma Cell Line U-266_Multiple_myeloma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/U-266/Multiple_myeloma/DNase-Hypersensitivity/NCMLS +S00CR241.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031318490130/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS +BP_Z-138_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Mantle_cell_lymphoma Cell Line Z-138_Mantle_cell_lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/Z-138/Mantle_cell_lymphoma/DNase-Hypersensitivity/NCMLS +S00CS041.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031318490130/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS +C0010K46.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Female_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C0010K/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS +S00CTZ41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031318490130/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS +C0011I43.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Female_50_55_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C0011I/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS +S00EPZ41.DNase.hotspot_v3.20141014.bed NCMLS DHS monocyte_-_T_0days Venous Blood monocyte_-_T_0days Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031324825721/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS +C001UY46.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Male_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C001UY/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS +S00HRJ41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406635321/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS +C004084E.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C00408/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS +S00HSH41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406635321/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS +C005PS4E.DNase.hotspot_v3.20130819.bed NCMLS DHS CD14_positive_CD16_negative_classical_monocyte Cord Blood CD14_positive_CD16_negative_classical_monocyte Female NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cord_blood/C005PS/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS +S00HTF41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406635321/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS +C005VG45.DNase.hotspot_v3.20130819.bed NCMLS DHS macrophage Venous Blood macrophage Male_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C005VG/macrophage/DNase-Hypersensitivity/NCMLS +S00JPF41.DNase.hotspot_v3.20141014.bed NCMLS DHS monocyte_-_T_0days Venous Blood monocyte_-_T_0days Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406634921/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS +C006NS47.DNase.hotspot_v3.20130819.bed NCMLS DHS CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell Cord Blood CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell Male NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cord_blood/C006NS/CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell/DNase-Hypersensitivity/NCMLS +S00JQD41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406634921/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS +C006UE47.DNase.hotspot_v3.20130819.bed NCMLS DHS macrophage Venous Blood macrophage Male_65_70_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C006UE/macrophage/DNase-Hypersensitivity/NCMLS +S00JRB41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406634921/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS +S001MJ48.DNase.hotspot_v3.20130819.bed NCMLS DHS inflammatory_macrophage Venous Blood inflammatory_macrophage Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS +S00JS941.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406634921/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS +S001MJ4A.DNase.hotspot_v3.20130819.bed NCMLS DHS inflammatory_macrophage Venous Blood inflammatory_macrophage Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS +bp_KARPAS-422_d01.DNase.hotspot_v3.20131126.bed NCMLS DHS Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma Cell Line KARPAS-422_Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/KARPAS-422/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS +S005FH41.DNase.hotspot_v3.20130819.bed NCMLS DHS Acute_myeloid_leukemia Bone Marrow Acute_myeloid_leukemia Female_70_75_years_Acute_Myeloid_leukaemia NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Bone_marrow/UMCG_2012-082/Acute_myeloid_leukemia/DNase-Hypersensitivity/NCMLS +bp_SU-DHL-5_d01.DNase.hotspot_v3.20131126.bed NCMLS DHS Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma Cell Line SU-DHL-5_Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/SU-DHL-5/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS +S00BXV41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031319896021/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS +S00BYT41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031319896021/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS From 71efcfc8c24addddfae79cd08451369c64b335f2 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Thu, 7 Apr 2016 18:11:40 +0100 Subject: [PATCH 17/26] Adding blueprint data for eforge v1.2 --- database/README.txt | 27 ++++++++++---------- database/blueprint.decode | 60 ++++++++++++++++++++++----------------------- database/load_450k_array.pl | 2 +- database/load_dataset.pl | 3 ++- 4 files changed, 47 insertions(+), 45 deletions(-) diff --git a/database/README.txt b/database/README.txt index 9c09a8b..2e53347 100755 --- a/database/README.txt +++ b/database/README.txt @@ -10,29 +10,30 @@ In summary, the steps are: Please refer to the help of init_db.pl for information about the different options -rm eforge_1.1.db -perl init_db.pl --db_name eforge_1.1.db +rm eforge_1.2.db +perl init_db.pl --db_name eforge_1.2.db 2. LOAD THE ARRAYS Please refer to the help of load_450k_array.pl for information about the different options -perl load_450k_array.pl --work_dir input +perl load_450k_array.pl --work_dir input --db_name eforge_1.2.db 3. LOAD THE DATASETS Please refer to the help of load_dataset.pl for information about the different options -perl load_dataset.pl --db_name eforge_1.1.db --tag erc --name 'Roadmap Epigenomics (2012 data) - DHS' --decode_file erc.decode --work_dir input/erc/ -perl load_dataset.pl --db_name eforge_1.1.db --tag encode --name 'ENCODE - DHS' --decode_file encode.decode --work_dir input/encode/ -perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-DHS --name 'Consolidated Roadmap Epigenomics - DHS' --decode_file erc2.decode --work_dir input/erc2/ -perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3K27me3 --name 'Consolidated Roadmap Epigenomics - H3K27me3' --decode_file erc2-H3K27me3.decode --work_dir input/erc2/ -perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3K36me3 --name 'Consolidated Roadmap Epigenomics - H3K36me3' --decode_file erc2-H3K36me3.decode --work_dir input/erc2/ -perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3K4me3 --name 'Consolidated Roadmap Epigenomics - H3K4me3' --decode_file erc2-H3K4me3.decode --work_dir input/erc2/ -perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3K9me3 --name 'Consolidated Roadmap Epigenomics - H3K9me3' --decode_file erc2-H3K9me3.decode --work_dir input/erc2/ -perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3K4me1 --name 'Consolidated Roadmap Epigenomics - H3K4me1' --decode_file erc2-H3K4me1.decode --work_dir input/erc2/ -perl load_dataset.pl --db_name eforge_1.1.db --tag erc2-H3-all --name 'Consolidated Roadmap Epigenomics - All H3 marks' --decode_file erc2-H3-all.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.2.db --tag erc --name 'Roadmap Epigenomics (2012 data) - DHS' --decode_file erc.decode --work_dir input/erc/ +perl load_dataset.pl --db_name eforge_1.2.db --tag encode --name 'ENCODE - DHS' --decode_file encode.decode --work_dir input/encode/ +perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-DHS --name 'Consolidated Roadmap Epigenomics - DHS' --decode_file erc2.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K27me3 --name 'Consolidated Roadmap Epigenomics - H3K27me3' --decode_file erc2-H3K27me3.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K36me3 --name 'Consolidated Roadmap Epigenomics - H3K36me3' --decode_file erc2-H3K36me3.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K4me3 --name 'Consolidated Roadmap Epigenomics - H3K4me3' --decode_file erc2-H3K4me3.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K9me3 --name 'Consolidated Roadmap Epigenomics - H3K9me3' --decode_file erc2-H3K9me3.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3K4me1 --name 'Consolidated Roadmap Epigenomics - H3K4me1' --decode_file erc2-H3K4me1.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.2.db --tag erc2-H3-all --name 'Consolidated Roadmap Epigenomics - All H3 marks' --decode_file erc2-H3-all.decode --work_dir input/erc2/ +perl load_dataset.pl --db_name eforge_1.2.db --tag blueprint --name 'Blueprint - DHS' --decode_file blueprint.decode --work_dir input/blueprint/ 4. MOVE THE DATABASE TO ITS FINAL LOCATION -mv eforge_1.1.db .. +mv eforge_1.2.db .. diff --git a/database/blueprint.decode b/database/blueprint.decode index f498876..eb41245 100644 --- a/database/blueprint.decode +++ b/database/blueprint.decode @@ -1,31 +1,31 @@ file lab datatype cell tissue shortcell individual acc url -BP_DG-75_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Sporadic_Burkitt_lymphoma Cell Line DG-75_Sporadic_Burkitt_lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/DG-75/Sporadic_Burkitt_lymphoma/DNase-Hypersensitivity/NCMLS -S00C0J41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031319896021/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS -BP_U-266_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Multiple_myeloma Cell Line U-266_Multiple_myeloma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/U-266/Multiple_myeloma/DNase-Hypersensitivity/NCMLS -S00CR241.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031318490130/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS -BP_Z-138_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Mantle_cell_lymphoma Cell Line Z-138_Mantle_cell_lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/Z-138/Mantle_cell_lymphoma/DNase-Hypersensitivity/NCMLS -S00CS041.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031318490130/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS -C0010K46.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Female_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C0010K/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS -S00CTZ41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031318490130/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS -C0011I43.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Female_50_55_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C0011I/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS -S00EPZ41.DNase.hotspot_v3.20141014.bed NCMLS DHS monocyte_-_T_0days Venous Blood monocyte_-_T_0days Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031324825721/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS -C001UY46.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Male_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C001UY/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS -S00HRJ41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406635321/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS -C004084E.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C00408/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS -S00HSH41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406635321/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS -C005PS4E.DNase.hotspot_v3.20130819.bed NCMLS DHS CD14_positive_CD16_negative_classical_monocyte Cord Blood CD14_positive_CD16_negative_classical_monocyte Female NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cord_blood/C005PS/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS -S00HTF41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406635321/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS -C005VG45.DNase.hotspot_v3.20130819.bed NCMLS DHS macrophage Venous Blood macrophage Male_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C005VG/macrophage/DNase-Hypersensitivity/NCMLS -S00JPF41.DNase.hotspot_v3.20141014.bed NCMLS DHS monocyte_-_T_0days Venous Blood monocyte_-_T_0days Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406634921/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS -C006NS47.DNase.hotspot_v3.20130819.bed NCMLS DHS CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell Cord Blood CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell Male NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cord_blood/C006NS/CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell/DNase-Hypersensitivity/NCMLS -S00JQD41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406634921/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS -C006UE47.DNase.hotspot_v3.20130819.bed NCMLS DHS macrophage Venous Blood macrophage Male_65_70_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/C006UE/macrophage/DNase-Hypersensitivity/NCMLS -S00JRB41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406634921/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS -S001MJ48.DNase.hotspot_v3.20130819.bed NCMLS DHS inflammatory_macrophage Venous Blood inflammatory_macrophage Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS -S00JS941.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031406634921/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS -S001MJ4A.DNase.hotspot_v3.20130819.bed NCMLS DHS inflammatory_macrophage Venous Blood inflammatory_macrophage Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS -bp_KARPAS-422_d01.DNase.hotspot_v3.20131126.bed NCMLS DHS Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma Cell Line KARPAS-422_Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/KARPAS-422/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS -S005FH41.DNase.hotspot_v3.20130819.bed NCMLS DHS Acute_myeloid_leukemia Bone Marrow Acute_myeloid_leukemia Female_70_75_years_Acute_Myeloid_leukaemia NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Bone_marrow/UMCG_2012-082/Acute_myeloid_leukemia/DNase-Hypersensitivity/NCMLS -bp_SU-DHL-5_d01.DNase.hotspot_v3.20131126.bed NCMLS DHS Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma Cell Line SU-DHL-5_Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Cell_Line/SU-DHL-5/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS -S00BXV41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031319896021/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS -S00BYT41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/Venous_blood/N00031319896021/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS +BP_DG-75_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Sporadic_Burkitt_lymphoma Cell Line DG-75_Sporadic_Burkitt_lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/DG-75/Sporadic_Burkitt_lymphoma/DNase-Hypersensitivity/NCMLS/BP_DG-75_d01.DNase.hotspot_v3.20130819.bed.gz +S00C0J41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031319896021/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS/S00C0J41.DNase.hotspot_v3.20141014.bed.gz +BP_U-266_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Multiple_myeloma Cell Line U-266_Multiple_myeloma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/U-266/Multiple_myeloma/DNase-Hypersensitivity/NCMLS/BP_U-266_d01.DNase.hotspot_v3.20130819.bed.gz +S00CR241.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031318490130/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS/S00CR241.DNase.hotspot_v3.20141014.bed.gz +BP_Z-138_d01.DNase.hotspot_v3.20130819.bed NCMLS DHS Mantle_cell_lymphoma Cell Line Z-138_Mantle_cell_lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/Z-138/Mantle_cell_lymphoma/DNase-Hypersensitivity/NCMLS/BP_Z-138_d01.DNase.hotspot_v3.20130819.bed.gz +S00CS041.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031318490130/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS/S00CS041.DNase.hotspot_v3.20141014.bed.gz +C0010K46.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Female_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C0010K/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C0010K46.DNase.hotspot_v3.20130415.bed.gz +S00CTZ41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031318490130/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS/S00CTZ41.DNase.hotspot_v3.20141014.bed.gz +C0011I43.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Female_50_55_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C0011I/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C0011I43.DNase.hotspot_v3.20130415.bed.gz +S00EPZ41.DNase.hotspot_v3.20141014.bed NCMLS DHS monocyte_-_T_0days Venous Blood monocyte_-_T_0days Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031324825721/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS/S00EPZ41.DNase.hotspot_v3.20141014.bed.gz +C001UY46.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Male_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C001UY/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C001UY46.DNase.hotspot_v3.20130415.bed.gz +S00HRJ41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406635321/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS/S00HRJ41.DNase.hotspot_v3.20141014.bed.gz +C004084E.DNase.hotspot_v3.20130415.bed NCMLS DHS CD14-positive_CD16-negative_classical_monocyte Venous Blood CD14-positive_CD16-negative_classical_monocyte Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C00408/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C004084E.DNase.hotspot_v3.20130415.bed.gz +S00HSH41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406635321/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS/S00HSH41.DNase.hotspot_v3.20141014.bed.gz +C005PS4E.DNase.hotspot_v3.20130819.bed NCMLS DHS CD14_positive_CD16_negative_classical_monocyte Cord Blood CD14_positive_CD16_negative_classical_monocyte Female NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cord_blood/C005PS/CD14-positive_CD16-negative_classical_monocyte/DNase-Hypersensitivity/NCMLS/C005PS4E.DNase.hotspot_v3.20130819.bed.gz +S00HTF41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Male_55_60_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406635321/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS/S00HTF41.DNase.hotspot_v3.20141014.bed.gz +C005VG45.DNase.hotspot_v3.20130819.bed NCMLS DHS macrophage Venous Blood macrophage Male_60_65_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C005VG/macrophage/DNase-Hypersensitivity/NCMLS/C005VG45.DNase.hotspot_v3.20130819.bed.gz +S00JPF41.DNase.hotspot_v3.20141014.bed NCMLS DHS monocyte_-_T_0days Venous Blood monocyte_-_T_0days Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406634921/monocyte_-_T_0days/DNase-Hypersensitivity/NCMLS/S00JPF41.DNase.hotspot_v3.20141014.bed.gz +C006NS47.DNase.hotspot_v3.20130819.bed NCMLS DHS CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell Cord Blood CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell Male NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cord_blood/C006NS/CD34-negative_CD41-positive_CD42-positive_megakaryocyte_cell/DNase-Hypersensitivity/NCMLS/C006NS47.DNase.hotspot_v3.20130819.bed.gz +S00JQD41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406634921/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS/S00JQD41.DNase.hotspot_v3.20141014.bed.gz +C006UE47.DNase.hotspot_v3.20130819.bed NCMLS DHS macrophage Venous Blood macrophage Male_65_70_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/C006UE/macrophage/DNase-Hypersensitivity/NCMLS/C006UE47.DNase.hotspot_v3.20130819.bed.gz +S00JRB41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406634921/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS/S00JRB41.DNase.hotspot_v3.20141014.bed.gz +S001MJ48.DNase.hotspot_v3.20130819.bed NCMLS DHS inflammatory_macrophage Venous Blood inflammatory_macrophage Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS/S001MJ48.DNase.hotspot_v3.20130819.bed.gz +S00JS941.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_B-glucan Venous Blood macrophage_-_T_6days_B-glucan Female_45_50_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031406634921/macrophage_-_T_6days_B-glucan/DNase-Hypersensitivity/NCMLS/S00JS941.DNase.hotspot_v3.20141014.bed.gz +S001MJ4A.DNase.hotspot_v3.20130819.bed NCMLS DHS inflammatory_macrophage Venous Blood inflammatory_macrophage Male_55_60_years NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/S001MJ/inflammatory_macrophage/DNase-Hypersensitivity/NCMLS/S001MJ4A.DNase.hotspot_v3.20130819.bed.gz +bp_KARPAS-422_d01.DNase.hotspot_v3.20131126.bed NCMLS DHS Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma Cell Line KARPAS-422_Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/KARPAS-422/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS/bp_KARPAS-422_d01.DNase.hotspot_v3.20131126.bed.gz +S005FH41.DNase.hotspot_v3.20130819.bed NCMLS DHS Acute_myeloid_leukemia Bone Marrow Acute_myeloid_leukemia Female_70_75_years_Acute_Myeloid_leukaemia NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Bone_marrow/UMCG_2012-082/Acute_myeloid_leukemia/DNase-Hypersensitivity/NCMLS/S005FH41.DNase.hotspot_v3.20130819.bed.gz +bp_SU-DHL-5_d01.DNase.hotspot_v3.20131126.bed NCMLS DHS Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma Cell Line SU-DHL-5_Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma NA NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Cell_Line/SU-DHL-5/Germinal_Center_B-Cell-Like_Diffuse_Large_B-Cell_Lymphoma/DNase-Hypersensitivity/NCMLS/bp_SU-DHL-5_d01.DNase.hotspot_v3.20131126.bed.gz +S00BXV41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_untreated Venous Blood macrophage_-_T_6days_untreated Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031319896021/macrophage_-_T_6days_untreated/DNase-Hypersensitivity/NCMLS/S00BXV41.DNase.hotspot_v3.20141014.bed.gz +S00BYT41.DNase.hotspot_v3.20141014.bed NCMLS DHS macrophage_-_T_6days_LPS Venous Blood macrophage_-_T_6days_LPS Female_30_35_years_Healthy NA ftp://ftp.ebi.ac.uk/pub/databases/blueprint/data/homo_sapiens/GRCh37/Venous_blood/N00031319896021/macrophage_-_T_6days_LPS/DNase-Hypersensitivity/NCMLS/S00BYT41.DNase.hotspot_v3.20141014.bed.gz diff --git a/database/load_450k_array.pl b/database/load_450k_array.pl index 65ff62d..cde3c49 100644 --- a/database/load_450k_array.pl +++ b/database/load_450k_array.pl @@ -7,7 +7,7 @@ use DBI; my $db_dir = "."; -my $db_name = "eforge_1.1.db"; +my $db_name = "eforge_1.2.db"; my $array_tag = "450k"; my $array_name = "Illumina Human 450k array"; my $species = "Homo sapiens"; diff --git a/database/load_dataset.pl b/database/load_dataset.pl index c984b0c..6c947d3 100644 --- a/database/load_dataset.pl +++ b/database/load_dataset.pl @@ -238,7 +238,8 @@ sub get_decode_table { $decode_record->{$header[$i]} = $data[$i]; } # Check that file and URL match - die $this_line if ($decode_record->{"url"} !~ $decode_record->{"file"}); + die "File: ".$decode_record->{"file"}."\nURL: ".$decode_record->{"url"}."\nOn line: $this_line" + if ($decode_record->{"url"} !~ $decode_record->{"file"}); $decode_record->{"file"} = $decode_record->{"url"}; $decode_record->{"file"} =~ s/.+\///g; push(@$decode_table, $decode_record); From 4c8b4d58552a1d08c3f51f3417db99e290651eeb Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Fri, 8 Apr 2016 11:22:55 +0100 Subject: [PATCH 18/26] More changes for v1.2 --- eforge.pl | 2 +- webserver/cgi-bin/index.pl | 12 ++++++++++++ 2 files changed, 13 insertions(+), 1 deletion(-) diff --git a/eforge.pl b/eforge.pl index de3c034..6a9dd51 100644 --- a/eforge.pl +++ b/eforge.pl @@ -183,7 +183,7 @@ =head1 ACKNOWLEDGEMENTS my $cwd = getcwd; -my $dbname = "eforge_1.1.db"; +my $dbname = "eforge_1.2.db"; my $bkgd; # Default value my $bkgd_label; diff --git a/webserver/cgi-bin/index.pl b/webserver/cgi-bin/index.pl index 2f32255..3d664c3 100755 --- a/webserver/cgi-bin/index.pl +++ b/webserver/cgi-bin/index.pl @@ -68,6 +68,7 @@ {"Download" => "$WEB_ROOT/?download"}, {"About" => "$WEB_ROOT/?about"}, {"__title__" => "Previous versions"}, + {"eFORGE v1.1" => "http://eforge.cs.ucl.ac.uk/eFORGE.v1.1"}, {"eFORGE v1.0" => "http://eforge.cs.ucl.ac.uk/eFORGE.v1.0"}, {"__title__" => "UCL Cancer Institute"}, {"Home" => "http://www.ucl.ac.uk/cancer/"}, @@ -999,6 +1000,17 @@ sub print_documentation_page { "<strong>False Positive Rate by DMP set Count</strong><br /><img src=\"$WEB_ROOT/img/analysis-fdr.png\" width=100%><br />This plot suggests that for a DMP set of >= 20, a threshold of -log10 (binomial p value) >= 3.38 (equivalent to 0.001 in corrected p value) maintains the false positive rate below around 0.0025 (0.25%)." ); + print Template::content_box("Versions", + "<strong>v1.2</strong><br \><br \> +This version includes DHS data from the BLUEPRINT Consortium.<br />", + + "<strong>v1.1</strong><br /><br /> +Version 1.1 adds both DHS and Histone marks from the Consolidated Roadmap data to eFORGE analysis. One of the options allows to run eFORGE against all five H3 marks at once. This version also includes new changes under the hood like a redeisgn of the underlying database.<br />", + + "<strong>v1.0</strong><br /><br /> +First version of eFORGE. The tools allows to analyses DMPs versus Epigenome Roadmap and ENCODE DHS.<br />" + ); + print Template::end; exit(0); } From 147a57d45b3cdbecaa5883f1246e05e7bda4b441 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Fri, 8 Apr 2016 11:56:24 +0100 Subject: [PATCH 19/26] Fixing deployment instructions for v1.2 --- webserver/INSTALL | 45 ++++++++++++++++++++++++--------------------- webserver/cgi-bin/index.pl | 7 ++++--- 2 files changed, 28 insertions(+), 24 deletions(-) diff --git a/webserver/INSTALL b/webserver/INSTALL index 8548b77..a2c92fa 100644 --- a/webserver/INSTALL +++ b/webserver/INSTALL @@ -25,6 +25,7 @@ webserver. wget http://eforge.cs.ucl.ac.uk/files/eforge.db wget http://eforge.cs.ucl.ac.uk/files/eforge_1.1.db + wget http://eforge.cs.ucl.ac.uk/files/eforge_1.2.db wget http://eforge.cs.ucl.ac.uk/files/mvp_450k_bins wget http://eforge.cs.ucl.ac.uk/files/mvp_27k_bins @@ -74,27 +75,29 @@ server by the server itself. 3.b. Create some directories for hosting the code, log and result files: - sudo mkdir /var/www/eFORGE.v1.1/ - cd /var/www/eFORGE.v1.1/ + sudo mkdir /var/www/eFORGE.v1.2/ + cd /var/www/eFORGE.v1.2/ sudo mkdir -p bin log cgi-bin html html/files sudo chown apache log html/files # the user under which you run apache (see the line "User" in # /etc/httpd/conf/httpd.conf) 3.c. Copy the webserver files to the right directories - sudo rsync -avPL ~/eFORGE/webserver/cgi-bin/ /var/www/eFORGE.v1.1/cgi-bin/ - sudo rsync -avPL ~/eFORGE/webserver/bin/ /var/www/eFORGE.v1.1/bin/ - sudo rsync -avPL ~/eFORGE/webserver/html/ /var/www/eFORGE.v1.1/html/ - sudo rsync -avPL ~/eFORGE/eforge.db /var/www/eFORGE.v1.1/bin/ - sudo rsync -avPL ~/eFORGE/eforge_1.1.db /var/www/eFORGE.v1.1/bin/ - sudo rsync -avPL ~/eFORGE/mvp_450k_bins /var/www/eFORGE.v1.1/bin/ - sudo rsync -avPL ~/eFORGE/mvp_27k_bins /var/www/eFORGE.v1.1/bin/ + sudo rsync -avPL ~/eFORGE/webserver/cgi-bin/ /var/www/eFORGE.v1.2/cgi-bin/ + sudo rsync -avPL ~/eFORGE/webserver/bin/ /var/www/eFORGE.v1.2/bin/ + sudo rsync -avPL ~/eFORGE/webserver/html/ /var/www/eFORGE.v1.2/html/ + sudo rsync -avPL ~/eFORGE/eforge.db /var/www/eFORGE.v1.2/bin/ + sudo rsync -avPL ~/eFORGE/eforge_1.1.db /var/www/eFORGE.v1.2/bin/ + sudo rsync -avPL ~/eFORGE/eforge_1.2.db /var/www/eFORGE.v1.2/bin/ + sudo rsync -avPL ~/eFORGE/mvp_450k_bins /var/www/eFORGE.v1.2/bin/ + sudo rsync -avPL ~/eFORGE/mvp_27k_bins /var/www/eFORGE.v1.2/bin/ 3.e. Add links to the database files for the Downloads page: - cd /var/www/eFORGE.v1.1/html/files + cd /var/www/eFORGE.v1.2/html/files sudo ln -s ../../bin/eforge.db . sudo ln -s ../../bin/eforge_1.1.db . + sudo ln -s ../../bin/eforge_1.2.db . sudo ln -s ../../bin/mvp_450k_bins . sudo ln -s ../../bin/mvp_27k_bins . @@ -103,7 +106,7 @@ server by the server itself. These files contain a list of arrays and dataset included in the database. They are used by the web server to know what it can offer without having to query the DB every time. - cd /var/www/eFORGE.v1.1/bin + cd /var/www/eFORGE.v1.2/bin perl eforge.pl -data ? > data.conf perl eforge.pl -bkgd ? > bkgd.conf @@ -114,22 +117,22 @@ folder (like http://blic.cs.ucl.ac.uk/eFORGE). OPTION 1 -- Configure an Apache VirtualHost for eFORGE: - cat > /etc/http/conf.d/eforge.v1.1.conf + cat > /etc/http/conf.d/eforge.v1.2.conf <VirtualHost *:80> ServerName eforge.cs.ucl.ac.uk - DocumentRoot /var/www/eFORGE/html - ScriptAlias /cgi-bin/ /var/www/eFORGE.v1.1/cgi-bin/ + DocumentRoot /var/www/eFORGE.v1.2./html + ScriptAlias /cgi-bin/ /var/www/eFORGE.v1.2/cgi-bin/ <IfModule dir_module> DirectoryIndex index.html /cgi-bin/index.pl </IfModule> - <Directory "/var/www/eFORGE.v1.1/html"> + <Directory "/var/www/eFORGE.v1.2/html"> Order allow,deny Allow from all </Directory> - <Directory "/var/www/eFORGE.v1.1/cgi-bin"> + <Directory "/var/www/eFORGE.v1.2/cgi-bin"> AllowOverride None Options None Order allow,deny @@ -140,18 +143,18 @@ OPTION 1 -- Configure an Apache VirtualHost for eFORGE: OPTION 2 -- Configure an Apache VirtualHost for eFORGE: - cat > /etc/http/conf.d/eforge.v1.1.conf -ScriptAlias /eFORGE.v1.1/cgi-bin/ /var/www/eFORGE.v1.1/cgi-bin/ -Alias "/eFORGE.v1.1" "/var/www/eFORGE.v1.1/html" + cat > /etc/http/conf.d/eforge.v1.2.conf +ScriptAlias /eFORGE.v1.2/cgi-bin/ /var/www/eFORGE.v1.2/cgi-bin/ +Alias "/eFORGE.v1.2" "/var/www/eFORGE.v1.2/html" -<Directory "/var/www/eFORGE.v1.1/html/"> +<Directory "/var/www/eFORGE.v1.2/html/"> Order allow,deny Allow from all DirectoryIndex index.html cgi-bin/index.pl </Directory> -<Directory "/var/www/eFORGE.v1.1/cgi-bin/"> +<Directory "/var/www/eFORGE.v1.2/cgi-bin/"> AllowOverride None Options None Order allow,deny diff --git a/webserver/cgi-bin/index.pl b/webserver/cgi-bin/index.pl index 3d664c3..1aceb44 100755 --- a/webserver/cgi-bin/index.pl +++ b/webserver/cgi-bin/index.pl @@ -25,13 +25,13 @@ ## # The location of the HTML pages for this server on the filesystem -my $DOCUMENT_ROOT = "/var/www/eFORGE.v1.1/html"; +my $DOCUMENT_ROOT = "/var/www/eFORGE.v1.2/html"; # The base URL (without the server name) for this server. For instance: # Running on http://server.org/ -> $WEB_ROOT = "" # Running on http://server.org/tool/ -> $WEB_ROOT = "/tool" # IMPORTANT - DO NOT INCLUDE A TRAILING '/' -my $WEB_ROOT = "/eFORGE.v1.1"; +my $WEB_ROOT = "/eFORGE.v1.2"; # The location of the files w.r.t. the base URL (DO NOT CHANGE) my $WEB_OUTDIR = "/files"; @@ -47,7 +47,7 @@ my $colour="bright-blue"; my $plot_colour="#29A6C9"; -my $title = "eFORGE v1.1"; +my $title = "eFORGE v1.2"; my $bkgd_conf = read_conf_file("$BIN_DIR/bkgd.conf"); @@ -1036,6 +1036,7 @@ sub print_download_page { "Additional files you will require: <ul><li><a href=\"$WEB_ROOT$WEB_OUTDIR/eforge.db\">eforge.db</a> (for eFORGE v1.0)</li> <li><a href=\"$WEB_ROOT$WEB_OUTDIR/eforge_1.1.db\">eforge_1.1.db</a> (for eFORGE v1.1)</li> + <li><a href=\"$WEB_ROOT$WEB_OUTDIR/eforge_1.2.db\">eforge_1.2.db</a> (for eFORGE v1.2)</li> <li><a href=\"$WEB_ROOT$WEB_OUTDIR/mvp_450k_bins\">mvp_450k_bins</a></li> <li><a href=\"$WEB_ROOT$WEB_OUTDIR/mvp_27k_bins\">mvp_27k_bins</a></li></ul>"); print Template::content_box("License", From 7bb586976cdfbd59f55c9dac5971f631ba605928 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Fri, 15 Apr 2016 17:29:07 +0100 Subject: [PATCH 20/26] Fix some typos --- webserver/INSTALL | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/webserver/INSTALL b/webserver/INSTALL index a2c92fa..4b2a4d9 100644 --- a/webserver/INSTALL +++ b/webserver/INSTALL @@ -117,7 +117,7 @@ folder (like http://blic.cs.ucl.ac.uk/eFORGE). OPTION 1 -- Configure an Apache VirtualHost for eFORGE: - cat > /etc/http/conf.d/eforge.v1.2.conf + cat > /etc/httpd/conf.d/eforge.v1.2.conf <VirtualHost *:80> ServerName eforge.cs.ucl.ac.uk DocumentRoot /var/www/eFORGE.v1.2./html @@ -143,7 +143,7 @@ OPTION 1 -- Configure an Apache VirtualHost for eFORGE: OPTION 2 -- Configure an Apache VirtualHost for eFORGE: - cat > /etc/http/conf.d/eforge.v1.2.conf + cat > /etc/httpd/conf.d/eforge.v1.2.conf ScriptAlias /eFORGE.v1.2/cgi-bin/ /var/www/eFORGE.v1.2/cgi-bin/ Alias "/eFORGE.v1.2" "/var/www/eFORGE.v1.2/html" @@ -164,7 +164,7 @@ Alias "/eFORGE.v1.2" "/var/www/eFORGE.v1.2/html" 3.h. Copy the rCharts libraries to the html path: - sudo rsync -avP /usr/lib64/R/library/rCharts/libraries /var/www/eFORGE.v1.1/html/ + sudo rsync -avP /usr/lib64/R/library/rCharts/libraries /var/www/eFORGE.v1.2/html/ 3.i Re-start Apache From 65b8af4d084af6d6ac335c1cd78155c77ea22dd9 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Fri, 15 Apr 2016 17:30:26 +0100 Subject: [PATCH 21/26] Use the full URL for R libs This allows the user to download the file and use the interactive table or chart. --- webserver/cgi-bin/index.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/webserver/cgi-bin/index.pl b/webserver/cgi-bin/index.pl index 1aceb44..6f0ba40 100755 --- a/webserver/cgi-bin/index.pl +++ b/webserver/cgi-bin/index.pl @@ -309,7 +309,7 @@ =head2 validate_form sub validate_form { my $data; - my $validated_args = ["--web", ($WEB_ROOT or "/")]; + my $validated_args = ["--web", $q->url(-base=>1).($WEB_ROOT or "/")]; my @error_messages; my $input_data; From fa557f9863c3b6aa3fd0bcb5614b6c1b616e0fb3 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Mon, 18 Apr 2016 11:00:29 +0100 Subject: [PATCH 22/26] Use compressed files to save space on the server --- eforge.pl | 31 ++++++++++++++++++++++--------- webserver/cgi-bin/index.pl | 22 +++++++++++----------- 2 files changed, 33 insertions(+), 20 deletions(-) diff --git a/eforge.pl b/eforge.pl index 6a9dd51..59914f1 100644 --- a/eforge.pl +++ b/eforge.pl @@ -366,7 +366,14 @@ =head1 ACKNOWLEDGEMENTS warn "You have specified p value filtering, but this isn't implemented for files of format $format. No filtering will happen." } } - open my $fh, "<", $file or die "cannot open file $file : $!"; + my $fh; + if ($file =~ /\.gz$/) { + open($fh, "gunzip -c $file |") or die "cannot open file $file : $!"; + } elsif ($file =~ /\.bz2$/) { + open($fh, "bunzip2 -c $file |") or die "cannot open file $file : $!"; + } else { + open($fh, "<$file") or die "cannot open file $file : $!"; + } $mvps = process_file($fh, $format, $dbh, $bkgd, $filter); } elsif (@mvplist) { @@ -508,7 +515,9 @@ =head1 ACKNOWLEDGEMENTS mkdir $out_dir; -open my $bfh, ">", "$out_dir/background.tsv" or die "Cannot open background.tsv"; +if (!$web) { + open(BACKGROUND, "| gzip -9 > $out_dir/background.tsv.gz") or die "Cannot open background.tsv"; +} @@ -519,7 +528,9 @@ =head1 ACKNOWLEDGEMENTS # above line sorts by the tissues alphabetically (from $tissues hash values) # ultimately want a data frame of names(results)<-c("Zscore", "Cell", "Tissue", "File", "MVPs") - say $bfh join("\t", @{$bkgrd{$cell}}); + if (!$web) { + print BACKGROUND join("\t", @{$bkgrd{$cell}}), "\n"; + } my $teststat = ($$test{'CELLS'}{$cell}{'COUNT'} or 0); #number of overlaps for the test MVPs # binomial pvalue, probability of success is derived from the background overlaps over the tests for this cell @@ -560,20 +571,22 @@ =head1 ACKNOWLEDGEMENTS push(@results, [$zscore, $pbinom, $shortcell, $$tissues{$cell}{'tissue'}, $$tissues{$cell}{'datatype'}, $$tissues{$cell}{'file'}, $mvp_string, $$tissues{$cell}{'acc'}]); } -close($bfh); +if (!$web) { + close(BACKGROUND); +} # Correct the p-values for multiple testing using the Benjamini-Yekutieli FDR control method my $qvalues = BY(\@pvalues); $qvalues = [map {sprintf("%.2e", $_)} @$qvalues]; # Write the results to a tab-separated file -my $filename = "$lab.chart.tsv"; -open my $ofh, ">", "$out_dir/$filename" or die "Cannot open $out_dir/$filename: $!"; -print $ofh join("\t", "Zscore", "Pvalue", "Cell", "Tissue", "Datatype", "File", "Probe", "Accession", "Qvalue"), "\n"; +my $filename = "$lab.chart.tsv.gz"; +open(TSV, "| gzip -9 > $out_dir/$filename") or die "Cannot open $out_dir/$filename: $!"; +print TSV join("\t", "Zscore", "Pvalue", "Cell", "Tissue", "Datatype", "File", "Probe", "Accession", "Qvalue"), "\n"; for (my $i = 0; $i < @results; $i++) { - print $ofh join("\t", @{$results[$i]}, $qvalues->[$i]), "\n"; + print TSV join("\t", @{$results[$i]}, $qvalues->[$i]), "\n"; } -close($ofh); +close(TSV); warn "[".scalar(localtime())."] Generating plots...\n"; diff --git a/webserver/cgi-bin/index.pl b/webserver/cgi-bin/index.pl index 6f0ba40..21e7863 100755 --- a/webserver/cgi-bin/index.pl +++ b/webserver/cgi-bin/index.pl @@ -40,7 +40,7 @@ # The location of the bin dir w.r.t. the cgi-bin dir (DO NOT CHANGE) my $BIN_DIR = "../bin"; # The name of the input data file -my $INPUT_DATAFILE = "input.txt"; +my $INPUT_DATAFILE = "input.txt.gz"; # The name of the output data file my $STDOUT_FILE = "output.txt"; @@ -432,7 +432,7 @@ sub validate_form { ## It seems like all the options are valid, so we can now store the input data in the output ## directory my $absolute_outdir = get_absolute_outdir(); - open(INPUT, ">$absolute_outdir/$INPUT_DATAFILE") or + open(INPUT, "| gzip -9 > $absolute_outdir/$INPUT_DATAFILE") or die "Cannot open $absolute_outdir/$INPUT_DATAFILE"; foreach my $this_line (@lines) { print INPUT $this_line, "\n"; @@ -562,19 +562,19 @@ sub print_result { my $web_outdir = get_web_outdir(); opendir(DIR, $absolute_outdir); - my @files = grep {/(.pdf|.html|.tsv|.R)$/} readdir(DIR); + my @files = grep {/(.pdf|.html|.tsv|.R|.gz|.bz2)$/} readdir(DIR); closedir(DIR); - my $table_file = (grep {/.table.html$/} @files)[0]; - my $table_R = (grep {/.table.R$/i} @files)[0]; - my $dchart_file = (grep {/.dchart.html$/} @files)[0]; - my $dchart_R = (grep {/.dchart.R$/i} @files)[0]; - my $tsv_file = (grep {/.chart.tsv$/} @files)[0]; - my $pdf_file = (grep {/.chart.pdf$/} @files)[0]; + my $table_file = (grep {/\.table\.html$/} @files)[0]; + my $table_R = (grep {/\.table\.R$/i} @files)[0]; + my $dchart_file = (grep {/\.dchart\.html$/} @files)[0]; + my $dchart_R = (grep {/\.dchart\.R$/i} @files)[0]; + my $tsv_file = (grep {/\.chart\.tsv(\.gz|\.bz2)?$/} @files)[0]; + my $pdf_file = (grep {/\.chart\.pdf$/} @files)[0]; my $pdf_R = (grep {/.chart.R$/i} @files)[0]; print $fh Template::content_box_1("Results", - "<a href=\"$web_outdir/$INPUT_DATAFILE\">Input data (txt)</a>", - "<a href=\"$web_outdir/$tsv_file\">Raw data (tsv)</a>", + "<a href=\"$web_outdir/$INPUT_DATAFILE\">Input data (txt.gz)</a>", + "<a href=\"$web_outdir/$tsv_file\">Raw data (tsv.gz)</a>", "<a href=\"$web_outdir/$pdf_file\">Static chart (PDF)</a>", "<a href=\"$web_outdir/$dchart_file\">Interactive chart (HTML)</a>", "<a href=\"$web_outdir/$table_file\">Interactive table (HTML)</a>", From df48b559ed74b65d398484755711f124a5154ce9 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Fri, 29 Apr 2016 17:47:51 +0100 Subject: [PATCH 23/26] Close CVS file --- database/load_450k_array.pl | 1 + 1 file changed, 1 insertion(+) diff --git a/database/load_450k_array.pl b/database/load_450k_array.pl index cde3c49..3dadd80 100644 --- a/database/load_450k_array.pl +++ b/database/load_450k_array.pl @@ -116,6 +116,7 @@ sub parse_450k_file { $array->{$probe_id} = [$probe_chr36, $probe_loc36, $probe_chr37, $probe_loc37, $this_gene_annotation, $this_cpg_annotation]; } + close(CSV); # foreach my $this_a (keys %$annotation) { #@gene_annotations) { # print $annotation->{$this_a}, "\t", $this_a, "\n"; # } From 503e103f8040a88c7039359375a7ac7cea8a90a7 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Mon, 9 May 2016 19:44:36 +0100 Subject: [PATCH 24/26] Fix DB name to be for eFORGE v1.2 --- database/init_db.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/database/init_db.pl b/database/init_db.pl index b431989..7dc4a81 100644 --- a/database/init_db.pl +++ b/database/init_db.pl @@ -6,7 +6,7 @@ use Getopt::Long; my $db_dir = "."; -my $db_name = "eforge_1.1.db"; +my $db_name = "eforge_1.2.db"; my $help; From 386dbe2a43832b5c85e8a4edbde42caac3f6fee2 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Mon, 9 May 2016 19:45:18 +0100 Subject: [PATCH 25/26] Include 27k array --- database/README.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/database/README.txt b/database/README.txt index 2e53347..e583945 100755 --- a/database/README.txt +++ b/database/README.txt @@ -18,6 +18,7 @@ perl init_db.pl --db_name eforge_1.2.db Please refer to the help of load_450k_array.pl for information about the different options perl load_450k_array.pl --work_dir input --db_name eforge_1.2.db +perl load_27k_array.pl --work_dir input --db_name eforge_1.2.db 3. LOAD THE DATASETS From e96ba5b360135475f3d9af21e16b617fd8b08fa0 Mon Sep 17 00:00:00 2001 From: Javier Herrero <javier.herrero@ucl.ac.uk> Date: Mon, 9 May 2016 19:45:39 +0100 Subject: [PATCH 26/26] Include 27k array --- database/load_27k_array.pl | 346 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 346 insertions(+) create mode 100644 database/load_27k_array.pl diff --git a/database/load_27k_array.pl b/database/load_27k_array.pl new file mode 100644 index 0000000..c5e8011 --- /dev/null +++ b/database/load_27k_array.pl @@ -0,0 +1,346 @@ +#! /usr/bin/env perl +use strict; +use warnings; + +use Getopt::Long; +use File::Spec qw(splitpath); +use DBI; + +my $db_dir = "."; +my $db_name = "eforge_1.2.db"; +my $array_tag = "27k"; +my $array_name = "Illumina Human 27k array (subset of 450k only)"; +my $species = "Homo sapiens"; +my $proxy_threshold = 1000; +my $illumina27k_bpm_file = 'ftp://webdata:webdata@ussd-ftp.illumina.com/downloads/ProductFiles/HumanMethylation27/humanmethylation27_270596_v1-2.bpm'; +my $illumina450k_csv_file = 'ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/ProductFiles/HumanMethylation450/HumanMethylation450_15017482_v1-2.csv'; +my $work_dir = "."; +my $bedtools = "bedtools"; + +my $help; + +my $desc = qq{load_27k_array.pl [options] + +DESCRIPTION: + +This script loads the subset of probe locations and annotations of the Illumina Human 27k +methylation array that are shared with the 450k array into the eFORGE database. + +Note that you *must* load the arrays before loading the datasets. If you want to include new arrays +at a later date, you will have to reload all the datasets again (i.e. you will have to re-start from +scratch). + +Optional arguments: + --db_name <name> + is the name of the SQLite file [def: $db_name] + --db_dir <path> + is the location of the SQLite file [def: $db_dir] + --work_dir <path> + is the location where temporary files will be downloaded/created [def: $work_dir] + --bedtools <name> + is the name of the bedtools executable you want to use [def: $bedtools] +}; + +GetOptions( + "help" => \$help, + "db_name=s" => \$db_name, + "db_dir=s" => \$db_dir, + "work_dir=s" => \$work_dir, + "bedtools=s" => \$bedtools, + ); + +my $dsn = "dbi:SQLite:dbname=$db_dir/$db_name"; +my $dbh = DBI->connect($dsn, "", "") or die $DBI::errstr; + +my ($vol, $path, $file) = File::Spec->splitpath($illumina450k_csv_file); + +if (!-e "$work_dir/$file") { + download_url($illumina450k_csv_file, $work_dir); +} + +my $array450k_info = parse_450k_file("$work_dir/$file"); + +my ($vol27k, $path27k, $file27k) = File::Spec->splitpath($illumina27k_bpm_file); + +if (!-e "$work_dir/$file27k") { + download_url($illumina27k_bpm_file, $work_dir); +} + +my $array27k_info = parse_27k_file("$work_dir/$file27k"); + +my $array_info = subset_array($array450k_info, $array27k_info); + +load_array($dbh, $db_name, $species, $array_tag, $array_name, $array_info); + +load_proxy_filter($dbh, $db_name, $array_tag, "GRCh37", $work_dir, $proxy_threshold); + +exit(); + + +sub download_url { + my ($url, $work_dir) = @_; + + print "Downloading $url...\n"; + system("wget -q -N -P $work_dir $url"); +} + + +sub parse_450k_file { + my ($illumina450k_csv_file) = @_; + my $array; + + open(CSV, $illumina450k_csv_file) or die; + my $annotation; + my @gene_annotations = ("TSS200", "TSS1500", "1stExon", "Body", "3'UTR", "5'UTR", "IGR"); + my $cpg_annotations = { + 'N_Shelf' => "Shelf_Shore", + 'S_Shelf' => "Shelf_Shore", + 'N_Shore' => "Shelf_Shore", + 'S_Shore' => "Shelf_Shore", + 'Island' => "Island"}; + while (<CSV>) { + chomp; + my @data = split(",", $_); + my $probe_id = $data[0]; + next if ($probe_id !~ /^cg/ and $probe_id !~ /^ch\./); + my $probe_chr37 = $data[11]; + my $probe_loc37 = $data[12]; + my $probe_chr36 = $data[14]; + my $probe_loc36 = $data[15]; + my $this_gene_annotation_arrayStr = $data[23]; + my $this_cpg_annotation = $data[25]?$cpg_annotations->{$data[25]}:"NA"; + + my $this_gene_annotation; + if (!defined($this_gene_annotation_arrayStr) or $this_gene_annotation_arrayStr eq "") { + $this_gene_annotation = "IGR"; + } else { + my @this_gene_annotations = split(";", $this_gene_annotation_arrayStr); + foreach my $this_a (@this_gene_annotations) { + if (grep {$_ eq $this_a} @gene_annotations) { + $this_gene_annotation = $this_a; + last; + } + } + } + + $annotation->{$this_gene_annotation."-".$this_cpg_annotation}++; + + $array->{$probe_id} = [$probe_chr36, $probe_loc36, $probe_chr37, $probe_loc37, $this_gene_annotation, $this_cpg_annotation]; + } + close(CSV); +# foreach my $this_a (keys %$annotation) { #@gene_annotations) { +# print $annotation->{$this_a}, "\t", $this_a, "\n"; +# } + + return $array; +} + + +sub parse_27k_file { + my ($illumina27k_bpm_file) = @_; + my $array; + + open(CSV, $illumina27k_bpm_file) or die; + my $block = ""; + while (<CSV>) { + if (/^\[(\w+)\]/) { + $block = $1; + } + next if ($block ne "Assay"); + + chomp; + my @data = split(",", $_); + my $probe_id = $data[0]; + my $name = $data[1]; + my $probe_chr36 = $data[8]; + my $probe_loc36 = $data[9]; + + if ($probe_id !~ /^cg/ and $probe_id !~ /^ch\./) { +# print "Skipping $probe_id\n"; + next; + } + if ($probe_id ne $name) { + print "ERROR: $probe_id ne $name\n"; + } + $array->{$probe_id} = [$probe_chr36, $probe_loc36]; + } + close(CSV); + + return $array; +} + +sub subset_array { + my ($full_array, $sub_array) = @_; + my $array; + foreach my $probe_id (keys %$full_array) { + if ($sub_array->{$probe_id}) { + $array->{$probe_id} = $full_array->{$probe_id}; + print "MISMATCH $probe_id\n" if (($full_array->{$probe_id}->[0] ne $sub_array->{$probe_id}->[0]) + or + ($full_array->{$probe_id}->[1] != $sub_array->{$probe_id}->[1])); + } + } + return $array; +} + + +sub load_array_1 { + my ($dbh, $code_name, $array_info) = @_; + + my $table_name = $code_name; + $table_name =~ s/\W//g; + $table_name = "array_$table_name"; + $dbh->do("CREATE TABLE IF NOT EXISTS $table_name (probe_id, location, gene_group, cgi_group)"); + + my $sth = $dbh->prepare("INSERT INTO array_$code_name VALUES (?, ?, ?, ?)"); + foreach my $this_probe_id (sort keys $array_info) { + my ($chr, $loc, $gene_group, $cgi_group) = @{$array_info->{$this_probe_id}}; + my $location = "$chr:$loc-$loc"; + $sth->execute($this_probe_id, $location, $gene_group, $cgi_group); + } + $sth->finish(); + + return $table_name; +} + + +sub load_array { + my ($dbh, $db_name, $species_name, $array_tag, $array_name, $array_info) = @_; + + my $sth; + $sth = $dbh->prepare("INSERT OR IGNORE INTO array (array_tag, array_name, species_name) VALUES (?, ?, ?)"); + $sth->execute($array_tag, $array_name, $species_name); + my $array_id = $dbh->last_insert_id("", "", "", ""); + $sth->finish(); + if ($array_id == 0) { + $array_id = $dbh->selectrow_array("SELECT array_id FROM array WHERE array_name = '$array_name' AND species_name = 'Homo sapiens'"); + } + + $sth = $dbh->prepare("INSERT OR IGNORE INTO assembly (species_name, assembly_name) VALUES (?, ?)"); + $sth->execute($species_name, "GRCh37"); + $sth->execute($species_name, "NCBI36"); + $sth->finish(); + my $human36_assembly_id = $dbh->selectrow_array("SELECT assembly_id FROM assembly WHERE species_name = 'Homo sapiens' AND assembly_name = 'NCBI36'"); + my $human37_assembly_id = $dbh->selectrow_array("SELECT assembly_id FROM assembly WHERE species_name = 'Homo sapiens' AND assembly_name = 'GRCh37'"); + + $sth = $dbh->prepare("INSERT OR IGNORE INTO probe_mapping_info (array_id, assembly_id, url) VALUES (?, ?, ?)"); + $sth->execute($array_id, $human36_assembly_id, ""); + my $probe_mapping_human36_id = $dbh->last_insert_id("", "", "", ""); + $sth->execute($array_id, $human37_assembly_id, ""); + my $probe_mapping_human37_id = $dbh->last_insert_id("", "", "", ""); + $sth->finish(); + + $sth = $dbh->prepare("INSERT OR IGNORE INTO probe_annotation_info (array_id, gene_reference_name, cgi_reference_name, url) VALUES (?, ?, ?, ?)"); + $sth->execute($array_id, "RefSeq", "UCSC CpG Islands", ""); +# my $probe_annotation_id = $dbh->last_insert_id("", "", "", ""); + $sth->finish(); + + open(CSV1, ">probe_mapping.csv") or die; + open(CSV2, ">probe_annotation.csv") or die; +# my $sth1 = $dbh->prepare("INSERT OR IGNORE INTO probe_mapping (probe_mapping_id, probe_id, chr_name, position) VALUES (?, ?, ?, ?)"); +# my $sth2 = $dbh->prepare("INSERT OR IGNORE INTO probe_annotation (probe_annotation_id, probe_id, gene_group, cgi_group) VALUES (?, ?, ?, ?)"); + foreach my $this_probe_id (sort keys $array_info) { + my ($chr36, $loc36, $chr37, $loc37, $gene_group, $cgi_group) = @{$array_info->{$this_probe_id}}; + print CSV1 join(",", $probe_mapping_human36_id, $this_probe_id, "chr$chr36", $loc36), "\n"; + print CSV1 join(",", $probe_mapping_human37_id, $this_probe_id, "chr$chr37", $loc37), "\n"; +# print CSV2 join(",", $probe_annotation_id, $array_id, $this_probe_id, $gene_group, $cgi_group), "\n"; + print CSV2 join(",", $array_id, $this_probe_id, $gene_group, $cgi_group), "\n"; +# $sth1->execute($probe_mapping_human36_id, $this_probe_id, "chr$chr36", $loc36) if ($probe_mapping_human36_id); +# $sth1->execute($probe_mapping_human37_id, $this_probe_id, "chr$chr37", $loc37) if ($probe_mapping_human37_id); +# $sth2->execute($probe_annotation_id, $this_probe_id, $gene_group, $cgi_group) if ($probe_annotation_id); + } + close(CSV1); + close(CSV2); + system("echo '.mode csv +.import probe_mapping.csv probe_mapping +.import probe_annotation.csv probe_annotation' | sqlite3 $db_name"); +# $sth1->finish(); +# $sth2->finish(); + +} + +sub load_proxy_filter { + my ($dbh, $db_name, $array_tag, $assembly_name, $work_dir, $distance_threshold) = @_; + + my $array_id = $dbh->selectrow_arrayref("SELECT array_id FROM array WHERE array_tag = '$array_tag'")->[0]; + my $bed_file = dump_array_bed_file($dbh, $array_id, $assembly_name, $work_dir); + my $this_output_bed_file = "$work_dir/array_${array_id}.proxy.bed"; + my $runstr = "$bedtools window -w $distance_threshold -a $bed_file -b $bed_file > $this_output_bed_file"; + system($runstr) == 0 or die "Error while running bedtools: $?"; + + my $sth = $dbh->prepare("INSERT OR IGNORE INTO proxy_filter_info (array_id, description) VALUES (?, ?)"); + $sth->execute($array_id, "Distance-based: 1kb"); + + open(BED, $this_output_bed_file) or die; + my $all_probes; + my $mapping_probes; + while (<BED>) { + chomp; + my ($chr1, $start1, $end1, $probe1, $chr2, $start2, $end2, $probe2) = split("\t", $_); + $all_probes->{$probe1} = 1; + if ($probe1 ne $probe2) { + $mapping_probes->{$probe1}->{$probe2} = 1; + } + } + close(BED); + open(CSV, ">proxy_filter.csv") or die; + foreach my $probe (sort keys %$all_probes) { + if (defined($mapping_probes->{$probe})) { + print CSV "$array_id,$probe,", join("|", sort keys %{$mapping_probes->{$probe}}), "\n"; + } else { + print CSV "$array_id,$probe,NONE\n"; + } + } + close(CSV); + system("echo '.mode csv +.import proxy_filter.csv proxy_filter' | sqlite3 $db_name"); + +} + +sub dump_array_bed_file { + my ($dbh, $this_array_id, $assembly_name, $work_dir) = @_; + my $sql = "SELECT probe_mapping_id + FROM probe_mapping_info + JOIN assembly USING (assembly_id) + WHERE array_id = $this_array_id + AND assembly_name = '$assembly_name'"; + my $probe_mapping_id = $dbh->selectrow_array($sql); + if (!$probe_mapping_id) { + die "Cannot find a mapping for array $this_array_id and assembly $assembly_name\n"; + } + + $sql = "SELECT probe_id, chr_name, position FROM probe_mapping WHERE probe_mapping_id = $probe_mapping_id"; + my $probes = $dbh->selectall_arrayref($sql); + + my $bed_file = "$work_dir/array_${this_array_id}.bed"; + open(BED, ">$bed_file") or die; + foreach my $this_probe (sort _sort_probes @$probes) { + print BED join("\t", $this_probe->[1], $this_probe->[2], $this_probe->[2]+1, $this_probe->[0]), "\n"; + } + close(BED); + + return $bed_file; +} + +sub _sort_probes { + my $chr_a = $a->[1]; + my $chr_b = $b->[1]; + my $loc_a = $a->[2]; + my $loc_b = $b->[2]; + $chr_a =~ s/chr//; + $chr_b =~ s/chr//; + if ($chr_a eq $chr_b) { + return $loc_a <=> $loc_b; + } elsif ($chr_a =~ /^\d/ and $chr_b =~ /^\d/) { + return $chr_a <=> $chr_b; + } elsif ($chr_a =~ /^\d/) { + return -1; + } elsif ($chr_b =~ /^\d/) { + return 1; + } else { + return $chr_a cmp $chr_b; + } +} + + +exit();