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1 parent e6d6f30 commit cc355f1fdf22316e25193c6ac7346d9c9a0d8988 @srobb1 committed Apr 30, 2013
Showing with 2 additions and 2 deletions.
  1. +2 −2 scripts/relocaTE.pl
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@@ -727,7 +727,7 @@ sub getHelp {
`mkdir -p $path/results/all_files`
#combine confident insertions to one file
-echo \"TE\tTSD\tExper\tchromosome\tinsertion_site\tstrand\tleft_flanking_read_count\tright_flanking_read_count\tleft_flanking_seq\tright_flanking_seq\tTE_orientation\" > $path/results/temp
+echo \"TE\tTSD\tExper\tinsertion_site\tstrand\tleft_flanking_read_count\tright_flanking_read_count\tleft_flanking_seq\tright_flanking_seq\" > $path/results/temp
for i in \`ls $path/results/*.$TE.confident_nonref_insert.txt\` ; do grep -v flanking_read_count \$i >> $path/results/temp ; done
mv $path/results/temp $path/results/$exper.$TE.confident_nonref.txt
mv $path/results/*.$TE.confident_nonref_insert.txt $path/results/all_files
@@ -781,7 +781,7 @@ sub getHelp {
##do it now
##combine and delete individual chr files for confident sites
print "Finishing and cleaning up\n";
-`echo \"TE\tTSD\tEper\tchromosome\tinsertion_site\tstrand\tleft_flanking_read_count\tright_flanking_read_count\tleft_flanking_seq\tright_flanking_seq\tTE_orientation\" > $path/results/temp`;
+`echo \"TE\tTSD\tEper\tinsertion_site\tstrand\tleft_flanking_read_count\tright_flanking_read_count\tleft_flanking_seq\tright_flanking_seq\" > $path/results/temp`;
my @files = `ls $path/results/*.$TE.confident_nonref_insert.txt`;
foreach my $file (@files) {
chomp $file;

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