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2015-07-28 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.1.0 20150727 (tag:rc)
* Bug fixes
1) Fixed issue #76: information about broad/narrow cutoff will be
correctly displayed.
2) Fixed issue #79: bdgopt extparam option is fixed.
3) Fixed issue #87: reference to cProb has been fixed as 'Prob'
for filterdup command.
3) Fixed issue #78, #88 and similar issue reported in MACS google
group: MACS2 now can correctly deal with multiple alignment files
for -t or -c. The 'finalize' function will be correctly
called. Multiple files option is enabled for filterdup,
randsample, predictd, pileup and refinepeak commands.
4) A related issue to #88, when BAMPE mode is used, PE pairs will
be sorted by leftmost then rightmost ends.
2015-04-20 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.1.0 20150420 (tag:rc)
* New commands
1) bdgopt: some convenient functions to modify bedGraph files.
2) cmbreps: Combine scores from two replicates. Including three
methods: 1. take the maximum; 2. take the average; 3. use Fisher's
method to combine two p-value scores. After that, user can use
bdgpeakcall to call peaks on combined scores.
* New features
1) callpeak and bdgpeakcall now can try to analyze the
relationship between p-values and number/length of peaks then
generate a summary to help users decide an appropriate cutoff.
2) callpeak now can accept fold-enrichment cutoff as a filter for
final peak calls.
* Performance
Now MACS2 runs about 3X as fast as previous version. Trade
clean python codes for speed... Now while processing 50M ChIP vs
50M control, it will take only 10 minutes.
* Bug fixes
1) Sampling function in BAMPE mode.
2) Callpeak while there are >= 2 input files for -t or -c.
3) While reading BAM/SAM, those secondary or supplementary
alignments will be correctly skipped.
4) Fixed issue #33: Explanation is added to callpeak --keep-dup
option that MACS2 will discard those SAM/BAM alignments with bit
1024 no matter how --keep-dup is set.
5) Fixed issue #49: setuptools is used intead of distutils
6) Fixed issue #51: fix the problem when using --trackline
argument when control file is absent.
7) Fixed issue #53: Use Use SAM/BAM CIGAR to find the 5' end of
read mapped to minus strand. Previous implementation will find
incorrect 5' end if there is indel in alignment.
8) Fixed issue #56: An incorrect sorting method used for BAMPE
mode which will cause incorrect filtering of duplicated reads. Now
fixed.
9) Issue #63: Merged from jayhesselberth@github, extsize now can
be 1.
10) Issue #71: Merged from aertslab@github, close file descriptor
after creating them with mkstemp().
2014-06-16 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.1.0 20140616 (tag:rc)
* callpeak module
"--ratio" is added to manually assign the scaling factor of ChIP
vs control, e.g. from NCIS. Thank Colin D and Dietmar Rieder for
implementing the patch file!
"--shift" is added to move cutting ends (5' end of reads) around,
in order to process DNAse-Seq data, e.g., use "--shift -100
--extsize 200" to get 200bps fragments around 5' ends. For general
ChIP-Seq data analysis, this option should be always set as
0. Thank Xi Chen and Anshul Kundaje for the discussions in user
group!
** Do not output negative fragment size from cross-correlation
analysis. Thank Alvin Qin for the feedback!
** --half-ext and --control-shift are removed. For complex read
shifting and extending, combine '--shift' and '--extsize'
options. For comparing two conditions, use 'bdgdiff' module
instead.
** a bug is fixed to output the last pileup value in bdg file
correctly.
* filterdup
A 'dry-run' option is added to only output numbers, including the
number of allowed duplicates, the total number of reads before and
after filtering duplicates and the estimated duplication
rate. Thank John Urban for the suggestion!
2013-12-16 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.10 20131216 (tag:alpha)
bug fixes and tweaks
* We changed license from Artistic License to 3-clauses BSD license.
Yes. Simpler the better.
* Process paired-end data with "-f BAMPE" without control
* GappedPeak output for --broad option has been fixed again to be
consistent with official UCSC format. We add 1bp pseudo-block to
left and/or right of broad region when necessary, so that you can
virtualize the regions without strong enrichment inside
successfully. In downstream analysis except for virtualization,
you may need to remove all 1bps blocks from gappedPeak file.
* diffpeak subcommand is temporarily disabled. Till we
re-implement it.
2013-10-28 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.10 20131028 (tag:alpha)
* callpeak --call-summits improvement
The smoothing window length has been fixed as fragment length
instead of short read length. The larger smoothing window will
grant better smoothing results and better sub-peak summits
detection.
* --outdir and --ofile options for almost all commands
Thank Björn Grüning for initially implementing these options!
Now, MACS2 will save results into a specified
directory by '--outdir' option, and/or save result into a
specified file by '--ofile' option. Note, in case '--ofile' is
available for a subcommand, '-o' now has been adjusted to be the
same as '--ofile' instead of '--o-prefix'.
Here is the list of changes. For more detail, use 'macs2 xxx -h'
for each subcommand:
** callpeak: --outdir
** diffpeak: Not implemented
** bdgpeakcall: --outdir and --ofile
** bdgbroadcall: --outdir and --ofile
** bdgcmp: --outdir and --ofile. While --ofile is used, the number
and the order of arguments for --ofile must be the same as for -m.
** bdgdiff: --outdir and --ofile
** filterdup: --outdir
** pileup: --outdir
** randsample: --outdir
** refinepeak: --outdir and --ofile
2013-09-15 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.10 20130915 (tag:alpha)
* callpeak Added a new option --buffer-size
This option is to tweak a previously hidden parameter that
controls the steps to increase array size for storing alignment
information. While in some rare cases, the number of
chromosomes/contigs/scaffolds is huge, the original default
setting will cause a huge memory waste. In these cases, we
recommend to decrease --buffer-size (e.g., 1000) to save memory,
although the decrease will slow process to read alignment files.
* an optimization to speed up pvalue-qvalue statistics
Previously, it took a hour to prepare p-q-table for 65M vs 65M
human TF library, and now it will take 10 minutes. It was due to a
single line of code to get a value from a numpy array ...
* fixed logLR bugs.
2013-07-31 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.10 20130731 (tag:alpha)
* callpeak --call-summits
Fix bugs causing callpeak --call-summits option generating extra
number of peaks and inconsistent peak boundaries comparing to
default option. Thank Ben Levinson!
* bdgcmp output
Fix bugs causing bdgcmp output logLR all in positive values. Now
'depletion' can be correctly represented as negative values.
* bdgdiff
Fix the behavior of bdgdiff module. Now it can take four
bedGraph files, then use logLR as cutoff to call differential
regions. Check command line of bdgdiff for detail.
2013-07-13 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.10 20130713 (tag:alpha)
* fix bugs while output broadPeak and gappedPeak.
Note. Those weak broad regions without any strong enrichment
regions inside won't be saved in gappedPeak file.
* bdgcmp -T and -C are merged into -S and description is updated.
Now, you can use it to override SPMR values in your input for
bdgcmp. To use SPMR (from 'callpeak --SPMR -B') while calculating
statistics will cause weird results ( in most cases, lower
significancy), and won't be consistent with MACS2 callpeak
behavior. So if you have SPMR bedGraphs, input the smaller/larger
sample size in MILLION according to 'callpeak --to-large' option.
2013-07-10 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.10 20130710 (tag:alpha)
* fix BED style output format of callpeak module:
1) without --broad: narrowPeak (BED6+4) and BED for summit will be
the output. Old BED format file won't be saved.
2) with --broad: broadPeak (BED6+3) for broad region and
gappedPeak (BED12+3) for chained enriched regions will be the
output. Old BED format, narrowPeak format, summit file won't be
saved.
* bdgcmp now can accept list of methods to calculate scores. So
you can run it once to generate multiple types of scores. Thank
Jon Urban for this suggestion!
* C codes are re-generated through Cython 0.19.1.
2013-05-21 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.10 20130520 (tag:alpha)
* broad peak calling modules are modified in order to report all
relexed regions even there is no strong enrichment inside.
2013-05-01 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.10 20130501 (tag:alpha)
* Memory usage is decreased to about 1/4-1/5 of previous usage
Now, the internal data structure and algorithm are both
re-organized, so that intermediate data wouldn't be saved in
memory. Intead they will be calculated on the fly. New MACS2 will
spend longer time (1.5 to 2 times) however it will use less memory
so can be more usable on small mem servers.
* --seed option is added to callpeak and randsample commands
Thank Mathieu Gineste for this suggestion!
2013-03-05 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.10 20130306 (tag:alpha)
* diffpeak module New module to detect differential binding sites
with more statistics.
* Introduced --refine-peaks
Calculates reads balancing to refine peak summits
* Ouput file names prefix
Correct encodePeak to narrowPeak, broadPeak to bed12.
2012-09-13 Benjamin Schiller <benjamin.schiller@ucsf.edu>, Tao Liu <taoliu@jimmy.harvard.edu>
MACS version 2.0.10 (tag:alpha not released)
* Introduced BAMPEParser
Reads PE data directly, requires bedtools for now
* Introduced --call-summits
Uses signal processing methods to call overlapping peaks
* Added --no-trackline
By default, files have descriptive tracklines now
* new refinepeak command (experimental)
This new function will use a similar method in SPP (wtd), to
analyze raw tag distribution in peak region, then redefine the
peak summit where plus and minus tags are evenly distributed
around.
* Changes to output *
cPeakDetect.pyx has full support for new print/write methods and
--call-peaks, BAMPEParser, and use of paired-end data
* Parser optimization
cParser.pyx is rewritten to use io.BufferedReader to speed
up. Speed is doubled.
Code is reorganized -- most of functions are inherited from
GenericParser class.
* Use cross-correlation to calculate fragment size
First, all pairs will be used in prediction for fragment
size. Previously, only no more than 1000 pairs are used. Second,
cross-correlation is used to find the best phase difference
between + and - tag pileups.
* Speed up p-value and q-value calculation
This part is ten times faster now. I am using a dictionary to
cache p-value results from Poisson CDF function. A bit more memory
will be used to increase speed. I hope this dictionary would not
explode since the possible pairs of ChIP signal and control lambda
are hugely redundant. Also, I rewrited part of q-value
calculation.
* Speed up peak detection
This part is about hundred of times faster now. Optimizations
include using Numpy functions as much as possible, and making loop
body as small as possible.
* Post-processing on differential calls
After macs2diff finds differential binding sites between two
conditions, it will try to annotate the peak calls from one of two
conditions, describe the changes ...
* Fragment size prediction in macs2diff
Now by default, macs2diff will try to use the average fragment
size from both condition 1 and condition 2 for tag extension and
peak calling. Previously, by default, it will use different sizes
unless --nomodel is specified.
Technically, I separate model building processes out. So macs2diff
will build fragment sizes for condition 1 and 2 in parallel (2
processes maximum), then perform 4-way comparisons in parallel (4
processes maximum).
* Diff score
Combine two p/qscore tracks together. At regions where condition 1
is higher than condition 2, score would be positive, otherwise,
negative.
* SAMParser and BAMParser
Bug fixed for paired-end sequencing data.
* BedGraph.pyx
Fixed a bug while calling peaks from BedGraph file. It previously
mistakenly output same peaks multiple times at the end of
chromosome.
2011-11-2 Tao Liu <taoliu@jimmy.harvard.edu>
MACS version 2.0.9 (tag:alpha)
* Auto fixation on predicted d is turned off by default!
Previous --off-auto is now default. MACS will not automatically
fix d less than 2 times of tag size according to
--shiftsize. While tag size is getting longer nowadays, it would
be easier to have d less than 2 times of tag size, however d may
still be meaningful and useful. Please judge it using your own
wisdom.
* Scaling issue
Now, the default scaling while treatment and input are unbalanced
has been adjusted. By default, larger sample will be scaled down
linearly to match the smaller sample. In this way, background
noise will be reduced more than real signals, so we expect to have
more specific results than the other way around (i.e. --to-large
is set).
Also, an alternative option to randomly sample larger data
(--down-sample) is provided to replace default linear
scaling. However, this option will cause results irresproducible,
so be careful.
* randsample script
A new script 'randsample' is added, which can randomly sample
certain percentage or number of tags.
* Peak summit
Now, MACS will decide peak summits according to pileup height
instead of qvalue scores. In this way, the summit may be more
accurate.
* Diff score
MACS calculate qvalue scores as differential scores. When compare
two conditions (saying A and B), the maximum qscore for comparing
A to B -- maxqscore_a2b, and for comparing B to A --maxqscore_b2a
will be computed. If maxqscore_a2b is bigger, the diff score is
+maxqscore_a2b, otherwise, diff score is -1*maxqscore_b2a.
2011-09-15 Tao Liu <taoliu@jimmy.harvard.edu>
MACS version 2.0.8 (tag:alpha)
* bin/macs2, bin/bdgbroadcall, MACS2/IO/cScoreTrack.pyx, MACS2/IO/cBedGraph.pyx
New script bdgbroadcall and the extra option '--broad' for macs2
script, can be used to call broad regions with a loose cutoff to
link nearby significant regions. The output is represented as
BED12 format.
* MACS2/IO/cScoreTrack.pyx
Fix q-value calculation to generate forcefully monotonic values.
* bin/eland*2bed, bin/sam2bed and bin/filterdup
They are combined to one more powerful script called
"filterdup". The script filterdup can filter duplicated reads
according to sequencing depth and genome size. The script can also
convert any format supported by MACS to BED format.
2011-08-21 Tao Liu <taoliu@jimmy.harvard.edu>
MACS version 2.0.7 (tag:alpha)
* bin/macsdiff renamed to bin/bdgdiff
Now this script will work as a low-level finetuning tool as bdgcmp
and bdgpeakcall.
* bin/macs2diff
A new script to take treatment and control files from two
condition, calculate fragment size, use local poisson to get
pvalues and BH process to get qvalues, then combine 4-ways result
to call differential sites.
This script can use upto 4 cpus to speed up 4-ways calculation. (
I am trying multiprocessing in python. )
* MACS2/Constants.py, MACS2/IO/cBedGraph.pyx,
MACS2/IO/cScoreTrack.pyx, MACS2/OptValidator.py,
MACS2/PeakModel.py, MACS2/cPeakDetect.pyx
All above files are modified for the new macs2diff script.
* bin/macs2, bin/macs2diff, MACS2/OptValidator.py
Now q-value 0.01 is the default cutoff. If -p is specified,
p-value cutoff will be used instead.
2011-07-25 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.6 (tag:alpha)
* bin/macsdiff
A script to call differential regions. A naive way is introduced
to find the regions where:
1. signal from condition 1 is larger than input 1 and condition 2 --
unique region in condition 1;
2. signal from condition 2 is larger than input 2 and condition 1
-- unique region in condition 2;
3. signal from condition 1 is larger than input 1, signal from
condition 2 is larger than input 2, however either signal from
condition 1 or 2 is not larger than the other.
Here 'larger' means the pvalue or qvalue from a Poisson test is
under certain cutoff.
(I will make another script to wrap up mulitple scripts for
differential calling)
2011-07-07 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.5 (tag:alpha)
* bin/macs2, MACS2/cPeakDetect.py, MACS2/IO/cScoreTrack.pyx,
MACS2/IO/cPeakIO.pyx
Use hash to store peak information. Add back the feature to deal
with data without control.
Fix bug which incorrectly allows small peaks at the end of
chromosomes.
* bin/bdgpeakcall, bin/bdgcmp
Fix bugs. bdgpeakcall can output encodePeak format.
2011-06-22 Tao Liu <taoliu@jimmy.harvard.edu>
MACS version 2.0.4 (tag:alpha)
* cPeakDetect.py
Fix a bug, correctly assign lambda_bg while --to-small is
set. Thanks Junya Seo!
Add rank and num of bp columns to pvalue-qvalue table.
* cScoreTrack.py
Fix bugs to correctly deal with peakless chromosomes. Thanks
Vaibhav Jain!
Use AFDR for independent tests instead.
* encodePeak
Now MACS can output peak coordinates together with pvalue, qvalue,
summit positions in a single encodePeak format (designed for
ENCODE project) file. This file can be loaded to UCSC
browser. Definition of some specific columns are: 5th:
int(-log10pvalue*10), 7th: fold-change, 8th: -log10pvalue, 9th:
-log10qvalue, 10th: relative summit position to peak start.
2011-06-19 Tao Liu <taoliu@jimmy.harvard.edu>
MACS version 2.0.3 (tag:alpha)
* Rich output with qvalue, fold enrichment, and pileup height
Calculate q-values using a refined Benjamini–Hochberg–Yekutieli
procedure:
http://en.wikipedia.org/wiki/False_discovery_rate#Dependent_tests
Now we have a similiar xls output file as before. The differences
from previous file are:
1. Summit now is absolute summit, instead of relative summit
position;
2. 'Pileup' is previous 'tag' column. It's the extended fragment
pileup at the peak summit;
3. We now use '-log10(pvalue)' instead of '-10log10(pvalue)', so
5.00 means 1e-5, simple and less confusing.
4. FDR column becomes '-log10(qvalue)' column.
5. The pileup, -log10pvalue, fold_enrichment and -log10qvalue are
the values at the peak summit.
* Extra output files
NAME_pqtable.txt contains pvalue and qvalue relationships.
NAME_treat_pvalue.bdg and NAME_treat_qvalue.bdg store -log10pvalue
and -log10qvalue scores in BedGraph format. Nearby regions with
the same value are not merged.
* Separation of FeatIO.py
Its content has been divided into cPeakIO.pyx, cBedGraph.pyx, and
cFixWidthTrack.pyx. A modified bedGraphTrackI class was
implemented to store pileup, local lambda, pvalue, and qvalue
alltogether in cScoreTrack.pyx.
* Experimental option --half-ext
Suggested by NPS algorithm, I added an experimental option
--half-ext to let MACS only extends ChIP fragment around its
middle point for only 1/2 d.
2011-06-12 Tao Liu <taoliu@jimmy.harvard.edu>
MACS version 2.0.2 (tag:alpha)
* macs2
Add an error check to see if there is no common chromosome names
from treatment file and control file
* cPeakDetect.pyx, cFeatIO.pyx, cPileup.pyx
Reduce memory usage by removing deepcopy() calls.
* Modify README documents and others.
2011-05-19 Tao Liu <taoliu@jimmy.harvard.edu>
MACS Version 2.0.1 (tag:alpha)
* cPileup.pyx, cPeakDetect.pyx and peak calling process
Jie suggested me a brilliant simple method to pileup fragments
into bedGraph track. It works extremely faster than the previous
function, i.e, faster than MACS1.3 or MACS1.4. So I can include
large local lambda calculation in MACSv2 now. Now I generate three
bedGraphs for d-size local bias, slocal-size and llocal-size local
bias, and calculate the maximum local bias as local lambda
bedGraph track.
Minor: add_loc in bedGraphTrackI now can correctly merge the
region with its preceding region if their value are the same.
* macs2
Add an option to shift control tags before extension. By default,
control tags will be extended to both sides regardless of strand
information.
2011-05-17 Tao Liu <taoliu@jimmy.harvard.edu>
MACS Version 2.0.0 (tag:alpha)
* Use bedGraph type to store data internally and externally.
We can have theoretically one-basepair resolution profiles. 10
times smaller in filesize and even smaller after converting to
bigWig for visualization.
* Peak calling process modified. Better peak boundary detection.
Extend ChIP tag to d, and pileup to have a ChIP bedGraph. Extend
Control tag to d and 1,000bp, and pileup to two bedGraphs. (1000bp
one will be averaged to d size) Then calculate the maximum value
of these two tracks and a global background, to have a
local-lambda bedGraph.
Use -10log10poisson_pvalue as scores to generate a score track
before peak calling.
A general peak calling based on a score cutoff, min length of peak
and max gap between nearby peaks.
* Option changes.
Wiggle file output is removed. Now we only support bedGraph
output. The generation of bedGraph is highly recommended since it
will not cost extra time. In other words, bedGraph generation is
internally run even you don't want to save bedGraphs on disk, due
to the peak calling algorithm in MACS v2.
* cProb.pyx
We now can calculate poisson pvalue in log space so that the score
(-10*log10pvalue) will not have a upper limit of 3100 due to
precision of float number.
* Cython is adopted to speed up Python code.
2011-02-28 Tao Liu <taoliu@jimmy.harvard.edu>
Small fixes
* Replaced with a newest WigTrackI class and fixed the wignorm script.
2011-02-21 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.4.0rc2 (Valentine)
* --single-wig option is renamed to --single-profile
* BedGraph output with --bdg or -B option.
The BedGraph output provides 1bp resolution fragment pileup
profile. File size is smaller than wig file. This option can be
combined with --single-profile option to produce a bedgraph file
for the whole genome. This option can also make --space,
--call-subpeaks invalid.
* Fix the description of --shiftsize to correctly state that the
value is 1/2 d (fragment size).
* Fix a bug in the call to __filter_w_control_tags when control is
not available.
* Fix a bug on --to-small option. Now it works as expected.
* Fix a bug while counting the tags in candidate peak region, an
extra tag may be included. (Thanks to Jake Biesinger!)
* Fix the bug for the peaks extended outside of chromosome
start. If the minus strand tag goes outside of chromosome start
after extension of d, it will be thrown out.
* Post-process script for a combined wig file:
The "wignorm" command can be called after a full run of MACS14 as
a postprocess. wignorm can calculate the local background from the
control wig file from MACS14, then use either foldchange,
-10*log10(pvalue) from possion test, or difference after asinh
transformation as the score to build a single wig track to
represent the binding strength. This script will take a
significant long time to process.
* --wigextend has been obsoleted.
2010-09-21 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.4.0rc1 (Starry Sky)
* Duplicate reads option
--keep-dup behavior is changed. Now user can specify how many
reads he/she wants to keep at the same genomic location. 'auto' to
let MACS decide the number based on binomial distribution, 'all'
to let MACS keep all reads.
* pvalue and FDR fixes (Thanks to Prof. Zhiping Weng)
By default, MACS will now scale the smaller dataset to the bigger
dataset. For instance, if IP has 10 million reads, and Input has 5
million, MACS will double the lambda value calculated from Input
reads while calling BOTH the positive peaks and negative
peaks. This will address the issue caused by unbalanced numbers of
reads from IP and Input. If --to-small is turned on, MACS will
scale the larger dataset to the smaller one. So from now on, if d
is fixed, then the peaks from a MACS call for A vs B should be
identical to the negative peaks from a B vs A.
2010-09-01 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.4.0beta (summer wishes)
* New features
** Model building
The default behavior in the model building step is slightly
changed. When MACS can't find enough pairs to build model
(implemented in alpha version) or the modeled fragment length is
less than 2 times of tag length (implemented in beta version),
MACS will use 2 times of --shiftsize value as fragment length in
the later analysis. --off-auto can turn off this default behavior.
** Redundant tag filtering
The IO module is rewritten. The redundant tag filtering process
becomes simpler and works as promise. The maximum allowed number
of tags at the exact same location is calculated from the
sequencing depth and genome size using a binomial distribution,
for both TREAMENT and CONTROL separately. ( previously only
TREATMENT is considered ) The exact same location means the same
coordination and the same strand. Then MACS will only keep at most
this number of tags at the exact same location in the following
analysis. An option --keep-dup can let MACS skip the filtering and
keep all the tags. However this may bring in a lot of sequencing
bias, so you may get many false positive peaks.
** Single wiggle mode
First thing to mention, this is not the score track that I
described before. By default, MACS generates wiggle files for
fragment pileup for every chromosomes separately. When you use
--single-wig option, MACS will generate a single wiggle file for
all the chromosomes so you will get a wig.gz for TREATMENT and
another wig.gz for CONTROL if available.
** Sniff -- automatic format detection
Now, by default or "-f AUTO", MACS will decide the input file
format automatically. Technically, it will try to read at most
1000 records for the first 10 non-comment lines. If it succeeds,
the format is decided. I recommend not to use AUTO and specify the
right format for your input files, unless you combine different
formats in a single MACS run.
* Options changes
--single-wig and --keep-dup are added. Check previous section in
ChangeLog for detail.
-f (--format) AUTO is now the default option.
--slocal default: 1000
--llocal default: 10000
* Bug fixed
Setup script will stop the installation if python version is not
python2.6 or python2.7.
Local lambda calculation has been changed back. MACS will check
peak_region, slocal( default 1K) and llocal (default 10K) for the
local bias. The previous 200bps default will cause MACS misses
some peaks where the input bias is very sharp.
sam2bed.py script is corrected.
Relative pos in xls output is fixed.
Parser for ELAND_export is fixed to pass some of the no match
lines. And elandexport2bed.py is fixed too. ( however I can't
guarantee that it works on any eland_export files. )
2010-06-04 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.4.0alpha2 (be smarter)
* Options changes
--gsize now provides shortcuts for common genomes, including
human, mouse, C. elegans and fruitfly.
--llocal now will be 5000 bps if there is no input file, so that
local lambda doesn't overkill enriched binding sites.
2010-06-02 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.4alpha (be smarter)
* Options changes
--tsize option is redesigned. MACS will use the first 10 lines of
the input to decide the tag size. If user specifies --tsize, it
will override the auto decided tsize.
--lambdaset is replaced by --slocal and --llocal which mean the
small local region and large local region.
--bw has no effect on the scan-window size now. It only affects the
paired-peaks model process.
* Model building
During the model building, MACS will pick out the enriched regions
which are not too high and not too low to build the paired-peak
model. Default the region is from fold 10 to fold 30. If MACS
fails to build the model, by default it will use the nomodel
settings, like shiftsize=100bps, to shift and extend each
tags. This behavior can be turned off by '--off-auto'.
* Output files
An extra file including all the summit positions are saved in
*_summits.bed file. An option '--call-subpeaks' will invoke
PeakSplitter developed by Mali Salmon to split wide peaks into
smaller subpeaks.
* Sniff ( will in beta )
Automatically recognize the input file format, so use can combine
different format in one MACS run.
Not implemented features/TODO:
* Algorithms ( in near future? )
MACS will try to refine the peak boundaries by calculating the
scores for every point in the candidate peak regions. The score
will be the -10*log(10,pvalue) on a local poisson distribution. A
cutoff specified by users (--pvalue) will be applied to find the
precise sub-peaks in the original candidate peak region. Peak
boudaries and peak summits positions will be saved in separate BED
files.
* Single wiggle track ( in near future? )
A single wiggle track will be generated to save the scores within
candidate peak regions in the 10bps resolution. The wiggle file
is in fixedStep format.
2009-10-16 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.7.1 (Oktoberfest, bug fixed #1)
* bin/Constants.py
Fixed typo. FCSTEP -> FESTEP
* lib/PeakDetect.py
The 'femax' attribute bug is fixed
2009-10-02 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.7 (Oktoberfest)
* bin/macs, lib/PeakDetect.py, lib/IO/__init__.py, lib/OptValidator.py
Enhancements by Peter Chines:
1. gzip files are supported.
2. when --diag is on, user can set the increment and endpoint for
fold enrichment analysis by setting --fe-step and --fe-max.
Enhancements by Davide Cittaro:
1. BAM and SAM formats are supported.
2. small changes in the header lines of wiggle output.
Enhancements by Me:
1. I added --fe-min option;
2. Bowtie ascii output with suffix ".map" is supported.
Bug fixed:
1. --nolambda bug is fixed. ( reported by Martin in JHU )
2. --diag bug is fixed. ( reported by Bogdan Tanasa )
3. Function to remove suffix '.fa' is fixed. ( reported by Jeff Johnston )
4. Some "fold change" have been changed to "fold enrichment".
2009-06-10 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.6.1 (default parameter change)
* bin/macs, lib/PeakDetect.py
"--oldfdr" is removed. The 'oldfdr' behaviour becomes
default. "--futurefdr" is added which can turn on the 'new' method
introduced in 1.3.6. By default it's off.
* lib/PeakDetect.py
Fixed a bug. p-value is corrected a little bit.
2009-05-11 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.6 (Birthday cake)
* bin/macs
"track name" is added to the header of BED output file.
Now the default peak detection method is to consider 5k and 10k
nearby regions in treatment data and peak location, 1k, 5k, and
10k regions in control data to calculate local bias. The old
method can be called through '--old' option.
Information about how many total/unique tags in treatment or
control will be saved in final .xls output.
* lib/IO/__init__.py
".fa" will be removed from input tag alignment so only the
chromosome names are kept.
WigTrackI class is added for Wiggle like data structure. (not used
now)
The parser for ELAND multi PET files has been fixed. Now the 5'
tag position for a pair will be kept, whereas in the previous
version, the middle points are kept.
* lib/IO/BinKeeper.py
BinKeeperI class is inspired by Jim Kent's library for UCSC genome
browser, which can quickly access certain region for values in a
large wiggle like data file. (not used now)
* lib/OptValidator.py
typo fixed.
* lib/PeakDetect.py
Now the default peak detection method is to consider 5k and 10k
nearby regions in treatment data and peak location, 1k, 5k, and
10k regions in control data to calculate local bias. The old
method can be called through '--old' option.
Two columns have beed added to BED output file. 4th column: peak
name; 5th column: peak score using -10log(10,pvalue) as score.
* setup.py
Add support to build a Mac App through 'setup.py py2app', or a
Windows executable through 'setup.py py2exe'. You need to install
py2app or py2exe package in order to use these functions.
2009-02-12 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.5 (local lambda fixed, typo fixed, model figure improved)
* PeakDetect.py
Now, besides 1k, 5k, 10k, MACS will also consider peak size region
in control data to calculate local lambda for each peak. Peak
calling results will be slightly different with previous version,
beware!
* OptValidator.py
Typo fixed, ELANDParser -> ELANDResultParser
* OutputWriter.py
Now, modeled d value will be shown on the model figure.
2009-01-06 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.4 (Happy New Year Version, bug fixed, ELAND multi/PET support)
* macs, IO/__init__.py, PeakDetect.py
Add support for ELAND multi format. Add support for Pair-End
experiment, in this case, 5'end and 3'end ELAND multi format files
are required for treatment or control data. See 00README file for
detail.
Add wigextend option.
Add petdist option for Pair-End Tag experiment, which is the best
distance between 5' and 3' tags.
* PeakDetect.py
Fixed a bug which cause the end positions of every peak region
incorrectly added by 1 bp. ( Thanks Mali Salmon!)
* OutputWriter.py
Fix bugs while generating wiggle files. The start position of
wiggle file is set to 1 instead of 0.
Fix a bug that every 10M bps, signals in the first 'd' range are
lower than actual. ( Thanks Mali Salmon!)
2008-12-03 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.3 (wiggle bugs fixed)
* OutputWriter.py
Fix bugs while generating wiggle files. 1. 'span=' is added to
'variableStep' line; 2. previously, every 10M bps, the coordinates
were wrongly shifted to the right for 'd' basepairs.
* macs, PeakDetect.py
Add an option to save wiggle files on different resolution.
2008-10-02 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.2 (tiny bugs fixed)
* IO/__init__.py
Fix 65536 -> 65535. ( Thank Joon)
* Prob.py
Improved for binomial function with extra large number. Imported
from Cistrome project.
* PeakDetect.py
If treatment channel misses reads in some chromosome included in
control channel, or vice versa, MACS will not exit. (Thank Shaun
Mahony)
Instead, MACS will fake a tag at position -1 when calling
treatment peaks vs control, but will ignore the chromosome while
calling negative peaks.
2008-09-04 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.1 (tiny bugs fixed version)
* Prob.py
Hyunjin Gene Shin contributed some codes to Prob.py. Now the
binomial functions can tolerate large and small numbers.
* IO/__init__.py
Parsers now split lines in BED/ELAND file using any
whitespaces. 'track' or 'browser' lines will be regarded as
comment lines. A bug fixed when throwing StrandFormatError. The
maximum redundant tag number at a single position can be no less
than 65536.
2008-07-15 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3 (naming clarification version)
* Naming clarification changes according to our manuscript:
'frag_len' is changed to 'd'.
'fold_change' is changed to 'fold_enrichment'.
Suggest '--bw' parameter to be determined by users from the real
sonication size.
Maximum FDR is 100% in the output file.
And other clarifications in 00README file and the documents on the
website.
* IO/__init__.py
If the redundant tag number at a single position is over 32767,
just remember 32767, instead of raising an overflow exception.
* setup.py
fixed a typo.
* PeakDetect.py
Bug fixed for diagnosis report.
2008-07-10 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.2.2gamma
* Serious bugs fix:
Poisson distribution CDF and inverse CDF functions are
corrected. They can produce right results even for huge lambda
now. So that the p-value and FDR values in the final excel sheet
are corrected.
IO package now can tolerate some rare cases; ELANDParser in IO
package is fixed. (Thank Bogdan)
* Improvement:
Reverse paired peaks in model are rejected. So there will be no
negative 'frag_len'. (Thank Bogdan)
* Features added:
Diagnosis function is completed. Which can output a table file for
users to estimate their sequencing depth.
2008-06-30 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.2
* Probe.py is added!
GSL is totally removed from MACS. Instead, I have implemented the
CDF and inverse CDF for poisson and binomial distribution purely
in python.
* Constants.py is added!
Organize constants used in MACS in the Constants.py file.
* All other files are modified!
Foldchange calculation is modified. Now the foldchange only be
calculated at the peak summit position instead of the whole peak
region. The values will be higher and more robust than before.
Features added:
1. MACS can save wiggle format files containing the tag number at
every 10 bp along the genome. Tags are shifted according to our
model before they are calculated.
2. Model building and local lambda calculation can be skipped with
certain options.
3. A diagnosis report can be generated through '--diag'
option. This report can help you get an assumption about the
sequencing saturation. This funtion is only in beta stage.
4. FDR calculation speed is highly improved.
2008-05-28 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.1
* TabIO, PeakModel.py ...
Bug fixed to let MACS tolerate some cases while there is no tag on
either plus strand or minus strand.
* setup.py
Check the version of python. If the version is lower than 2.4,
refuse to install with warning.
2013-07-31 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.10 20130731 (tag:alpha)
* callpeak --call-summits
Fix bugs causing callpeak --call-summits option generating extra
number of peaks and inconsistent peak boundaries comparing to
default option. Thank Ben Levinson!
* bdgcmp output
Fix bugs causing bdgcmp output logLR all in positive values. Now
'depletion' can be correctly represented as negative values.
* bdgdiff
Fix the behavior of bdgdiff module. Now it can take four
bedGraph files, then use logLR as cutoff to call differential
regions. Check command line of bdgdiff for detail.
2013-07-13 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.10 20130713 (tag:alpha)
* fix bugs while output broadPeak and gappedPeak.
Note. Those weak broad regions without any strong enrichment
regions inside won't be saved in gappedPeak file.
* bdgcmp -T and -C are merged into -S and description is updated.
Now, you can use it to override SPMR values in your input for
bdgcmp. To use SPMR (from 'callpeak --SPMR -B') while calculating
statistics will cause weird results ( in most cases, lower
significancy), and won't be consistent with MACS2 callpeak
behavior. So if you have SPMR bedGraphs, input the smaller/larger
sample size in MILLION according to 'callpeak --to-large' option.
2013-07-10 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.10 20130710 (tag:alpha)
* fix BED style output format of callpeak module:
1) without --broad: narrowPeak (BED6+4) and BED for summit will be
the output. Old BED format file won't be saved.
2) with --broad: broadPeak (BED6+3) for broad region and
gappedPeak (BED12+3) for chained enriched regions will be the
output. Old BED format, narrowPeak format, summit file won't be
saved.
* bdgcmp now can accept list of methods to calculate scores. So
you can run it once to generate multiple types of scores. Thank
Jon Urban for this suggestion!
* C codes are re-generated through Cython 0.19.1.
2013-05-21 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.10 20130520 (tag:alpha)
* broad peak calling modules are modified in order to report all
relexed regions even there is no strong enrichment inside.
2013-05-01 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.10 20130501 (tag:alpha)
* Memory usage is decreased to about 1/4-1/5 of previous usage
Now, the internal data structure and algorithm are both
re-organized, so that intermediate data wouldn't be saved in
memory. Intead they will be calculated on the fly. New MACS2 will
spend longer time (1.5 to 2 times) however it will use less memory
so can be more usable on small mem servers.
* --seed option is added to callpeak and randsample commands
Thank Mathieu Gineste for this suggestion!
2013-03-05 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.10 20130306 (tag:alpha)
* diffpeak module New module to detect differential binding sites
with more statistics.
* Introduced --refine-peaks
Calculates reads balancing to refine peak summits
* Ouput file names prefix
Correct encodePeak to narrowPeak, broadPeak to bed12.
2012-09-13 Benjamin Schiller <benjamin.schiller@ucsf.edu>, Tao Liu <taoliu@jimmy.harvard.edu>
MACS version 2.0.10 (tag:alpha not released)
* Introduced BAMPEParser
Reads PE data directly, requires bedtools for now
* Introduced --call-summits
Uses signal processing methods to call overlapping peaks
* Added --no-trackline
By default, files have descriptive tracklines now
* new refinepeak command (experimental)
This new function will use a similar method in SPP (wtd), to
analyze raw tag distribution in peak region, then redefine the
peak summit where plus and minus tags are evenly distributed
around.
* Changes to output *
cPeakDetect.pyx has full support for new print/write methods and
--call-peaks, BAMPEParser, and use of paired-end data
* Parser optimization
cParser.pyx is rewritten to use io.BufferedReader to speed
up. Speed is doubled.
Code is reorganized -- most of functions are inherited from
GenericParser class.
* Use cross-correlation to calculate fragment size
First, all pairs will be used in prediction for fragment
size. Previously, only no more than 1000 pairs are used. Second,
cross-correlation is used to find the best phase difference
between + and - tag pileups.
* Speed up p-value and q-value calculation
This part is ten times faster now. I am using a dictionary to
cache p-value results from Poisson CDF function. A bit more memory
will be used to increase speed. I hope this dictionary would not
explode since the possible pairs of ChIP signal and control lambda
are hugely redundant. Also, I rewrited part of q-value
calculation.
* Speed up peak detection
This part is about hundred of times faster now. Optimizations
include using Numpy functions as much as possible, and making loop
body as small as possible.
* Post-processing on differential calls
After macs2diff finds differential binding sites between two
conditions, it will try to annotate the peak calls from one of two
conditions, describe the changes ...
* Fragment size prediction in macs2diff
Now by default, macs2diff will try to use the average fragment
size from both condition 1 and condition 2 for tag extension and
peak calling. Previously, by default, it will use different sizes
unless --nomodel is specified.
Technically, I separate model building processes out. So macs2diff
will build fragment sizes for condition 1 and 2 in parallel (2
processes maximum), then perform 4-way comparisons in parallel (4
processes maximum).
* Diff score
Combine two p/qscore tracks together. At regions where condition 1
is higher than condition 2, score would be positive, otherwise,
negative.
* SAMParser and BAMParser
Bug fixed for paired-end sequencing data.
* BedGraph.pyx
Fixed a bug while calling peaks from BedGraph file. It previously
mistakenly output same peaks multiple times at the end of
chromosome.
2011-11-2 Tao Liu <taoliu@jimmy.harvard.edu>
MACS version 2.0.9 (tag:alpha)
* Auto fixation on predicted d is turned off by default!
Previous --off-auto is now default. MACS will not automatically
fix d less than 2 times of tag size according to
--shiftsize. While tag size is getting longer nowadays, it would
be easier to have d less than 2 times of tag size, however d may
still be meaningful and useful. Please judge it using your own
wisdom.
* Scaling issue
Now, the default scaling while treatment and input are unbalanced
has been adjusted. By default, larger sample will be scaled down
linearly to match the smaller sample. In this way, background
noise will be reduced more than real signals, so we expect to have
more specific results than the other way around (i.e. --to-large
is set).
Also, an alternative option to randomly sample larger data
(--down-sample) is provided to replace default linear
scaling. However, this option will cause results irresproducible,
so be careful.
* randsample script
A new script 'randsample' is added, which can randomly sample
certain percentage or number of tags.
* Peak summit
Now, MACS will decide peak summits according to pileup height
instead of qvalue scores. In this way, the summit may be more
accurate.
* Diff score
MACS calculate qvalue scores as differential scores. When compare
two conditions (saying A and B), the maximum qscore for comparing
A to B -- maxqscore_a2b, and for comparing B to A --maxqscore_b2a
will be computed. If maxqscore_a2b is bigger, the diff score is
+maxqscore_a2b, otherwise, diff score is -1*maxqscore_b2a.
2011-09-15 Tao Liu <taoliu@jimmy.harvard.edu>
MACS version 2.0.8 (tag:alpha)
* bin/macs2, bin/bdgbroadcall, MACS2/IO/cScoreTrack.pyx, MACS2/IO/cBedGraph.pyx
New script bdgbroadcall and the extra option '--broad' for macs2
script, can be used to call broad regions with a loose cutoff to
link nearby significant regions. The output is represented as
BED12 format.
* MACS2/IO/cScoreTrack.pyx
Fix q-value calculation to generate forcefully monotonic values.
* bin/eland*2bed, bin/sam2bed and bin/filterdup
They are combined to one more powerful script called
"filterdup". The script filterdup can filter duplicated reads
according to sequencing depth and genome size. The script can also
convert any format supported by MACS to BED format.
2011-08-21 Tao Liu <taoliu@jimmy.harvard.edu>
MACS version 2.0.7 (tag:alpha)
* bin/macsdiff renamed to bin/bdgdiff
Now this script will work as a low-level finetuning tool as bdgcmp
and bdgpeakcall.
* bin/macs2diff
A new script to take treatment and control files from two
condition, calculate fragment size, use local poisson to get
pvalues and BH process to get qvalues, then combine 4-ways result
to call differential sites.
This script can use upto 4 cpus to speed up 4-ways calculation. (
I am trying multiprocessing in python. )
* MACS2/Constants.py, MACS2/IO/cBedGraph.pyx,
MACS2/IO/cScoreTrack.pyx, MACS2/OptValidator.py,
MACS2/PeakModel.py, MACS2/cPeakDetect.pyx
All above files are modified for the new macs2diff script.
* bin/macs2, bin/macs2diff, MACS2/OptValidator.py
Now q-value 0.01 is the default cutoff. If -p is specified,
p-value cutoff will be used instead.
2011-07-25 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.6 (tag:alpha)
* bin/macsdiff
A script to call differential regions. A naive way is introduced
to find the regions where:
1. signal from condition 1 is larger than input 1 and condition 2 --
unique region in condition 1;
2. signal from condition 2 is larger than input 2 and condition 1
-- unique region in condition 2;
3. signal from condition 1 is larger than input 1, signal from
condition 2 is larger than input 2, however either signal from
condition 1 or 2 is not larger than the other.
Here 'larger' means the pvalue or qvalue from a Poisson test is
under certain cutoff.
(I will make another script to wrap up mulitple scripts for
differential calling)
2011-07-07 Tao Liu <vladimir.liu@gmail.com>
MACS version 2.0.5 (tag:alpha)
* bin/macs2, MACS2/cPeakDetect.py, MACS2/IO/cScoreTrack.pyx,
MACS2/IO/cPeakIO.pyx
Use hash to store peak information. Add back the feature to deal
with data without control.
Fix bug which incorrectly allows small peaks at the end of
chromosomes.
* bin/bdgpeakcall, bin/bdgcmp
Fix bugs. bdgpeakcall can output encodePeak format.
2011-06-22 Tao Liu <taoliu@jimmy.harvard.edu>
MACS version 2.0.4 (tag:alpha)
* cPeakDetect.py
Fix a bug, correctly assign lambda_bg while --to-small is
set. Thanks Junya Seo!
Add rank and num of bp columns to pvalue-qvalue table.
* cScoreTrack.py
Fix bugs to correctly deal with peakless chromosomes. Thanks
Vaibhav Jain!
Use AFDR for independent tests instead.
* encodePeak
Now MACS can output peak coordinates together with pvalue, qvalue,
summit positions in a single encodePeak format (designed for
ENCODE project) file. This file can be loaded to UCSC
browser. Definition of some specific columns are: 5th:
int(-log10pvalue*10), 7th: fold-change, 8th: -log10pvalue, 9th:
-log10qvalue, 10th: relative summit position to peak start.
2011-06-19 Tao Liu <taoliu@jimmy.harvard.edu>
MACS version 2.0.3 (tag:alpha)
* Rich output with qvalue, fold enrichment, and pileup height
Calculate q-values using a refined Benjamini–Hochberg–Yekutieli
procedure:
http://en.wikipedia.org/wiki/False_discovery_rate#Dependent_tests
Now we have a similiar xls output file as before. The differences
from previous file are:
1. Summit now is absolute summit, instead of relative summit
position;
2. 'Pileup' is previous 'tag' column. It's the extended fragment
pileup at the peak summit;
3. We now use '-log10(pvalue)' instead of '-10log10(pvalue)', so
5.00 means 1e-5, simple and less confusing.
4. FDR column becomes '-log10(qvalue)' column.
5. The pileup, -log10pvalue, fold_enrichment and -log10qvalue are
the values at the peak summit.
* Extra output files
NAME_pqtable.txt contains pvalue and qvalue relationships.
NAME_treat_pvalue.bdg and NAME_treat_qvalue.bdg store -log10pvalue
and -log10qvalue scores in BedGraph format. Nearby regions with
the same value are not merged.
* Separation of FeatIO.py
Its content has been divided into cPeakIO.pyx, cBedGraph.pyx, and
cFixWidthTrack.pyx. A modified bedGraphTrackI class was
implemented to store pileup, local lambda, pvalue, and qvalue
alltogether in cScoreTrack.pyx.
* Experimental option --half-ext
Suggested by NPS algorithm, I added an experimental option
--half-ext to let MACS only extends ChIP fragment around its
middle point for only 1/2 d.
2011-06-12 Tao Liu <taoliu@jimmy.harvard.edu>
MACS version 2.0.2 (tag:alpha)
* macs2
Add an error check to see if there is no common chromosome names
from treatment file and control file
* cPeakDetect.pyx, cFeatIO.pyx, cPileup.pyx
Reduce memory usage by removing deepcopy() calls.
* Modify README documents and others.
2011-05-19 Tao Liu <taoliu@jimmy.harvard.edu>
MACS Version 2.0.1 (tag:alpha)
* cPileup.pyx, cPeakDetect.pyx and peak calling process
Jie suggested me a brilliant simple method to pileup fragments
into bedGraph track. It works extremely faster than the previous
function, i.e, faster than MACS1.3 or MACS1.4. So I can include
large local lambda calculation in MACSv2 now. Now I generate three
bedGraphs for d-size local bias, slocal-size and llocal-size local
bias, and calculate the maximum local bias as local lambda
bedGraph track.
Minor: add_loc in bedGraphTrackI now can correctly merge the
region with its preceding region if their value are the same.
* macs2
Add an option to shift control tags before extension. By default,
control tags will be extended to both sides regardless of strand
information.
2011-05-17 Tao Liu <taoliu@jimmy.harvard.edu>
MACS Version 2.0.0 (tag:alpha)
* Use bedGraph type to store data internally and externally.
We can have theoretically one-basepair resolution profiles. 10
times smaller in filesize and even smaller after converting to
bigWig for visualization.
* Peak calling process modified. Better peak boundary detection.
Extend ChIP tag to d, and pileup to have a ChIP bedGraph. Extend
Control tag to d and 1,000bp, and pileup to two bedGraphs. (1000bp
one will be averaged to d size) Then calculate the maximum value
of these two tracks and a global background, to have a
local-lambda bedGraph.
Use -10log10poisson_pvalue as scores to generate a score track
before peak calling.
A general peak calling based on a score cutoff, min length of peak
and max gap between nearby peaks.
* Option changes.
Wiggle file output is removed. Now we only support bedGraph
output. The generation of bedGraph is highly recommended since it
will not cost extra time. In other words, bedGraph generation is
internally run even you don't want to save bedGraphs on disk, due
to the peak calling algorithm in MACS v2.
* cProb.pyx
We now can calculate poisson pvalue in log space so that the score
(-10*log10pvalue) will not have a upper limit of 3100 due to
precision of float number.
* Cython is adopted to speed up Python code.
2011-02-28 Tao Liu <taoliu@jimmy.harvard.edu>
Small fixes
* Replaced with a newest WigTrackI class and fixed the wignorm script.
2011-02-21 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.4.0rc2 (Valentine)
* --single-wig option is renamed to --single-profile
* BedGraph output with --bdg or -B option.
The BedGraph output provides 1bp resolution fragment pileup
profile. File size is smaller than wig file. This option can be
combined with --single-profile option to produce a bedgraph file
for the whole genome. This option can also make --space,
--call-subpeaks invalid.
* Fix the description of --shiftsize to correctly state that the
value is 1/2 d (fragment size).
* Fix a bug in the call to __filter_w_control_tags when control is
not available.
* Fix a bug on --to-small option. Now it works as expected.
* Fix a bug while counting the tags in candidate peak region, an
extra tag may be included. (Thanks to Jake Biesinger!)
* Fix the bug for the peaks extended outside of chromosome
start. If the minus strand tag goes outside of chromosome start
after extension of d, it will be thrown out.
* Post-process script for a combined wig file:
The "wignorm" command can be called after a full run of MACS14 as
a postprocess. wignorm can calculate the local background from the
control wig file from MACS14, then use either foldchange,
-10*log10(pvalue) from possion test, or difference after asinh
transformation as the score to build a single wig track to
represent the binding strength. This script will take a
significant long time to process.
* --wigextend has been obsoleted.
2010-09-21 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.4.0rc1 (Starry Sky)
* Duplicate reads option
--keep-dup behavior is changed. Now user can specify how many
reads he/she wants to keep at the same genomic location. 'auto' to
let MACS decide the number based on binomial distribution, 'all'
to let MACS keep all reads.
* pvalue and FDR fixes (Thanks to Prof. Zhiping Weng)
By default, MACS will now scale the smaller dataset to the bigger
dataset. For instance, if IP has 10 million reads, and Input has 5
million, MACS will double the lambda value calculated from Input
reads while calling BOTH the positive peaks and negative
peaks. This will address the issue caused by unbalanced numbers of
reads from IP and Input. If --to-small is turned on, MACS will
scale the larger dataset to the smaller one. So from now on, if d
is fixed, then the peaks from a MACS call for A vs B should be
identical to the negative peaks from a B vs A.
2010-09-01 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.4.0beta (summer wishes)
* New features
** Model building
The default behavior in the model building step is slightly
changed. When MACS can't find enough pairs to build model
(implemented in alpha version) or the modeled fragment length is
less than 2 times of tag length (implemented in beta version),
MACS will use 2 times of --shiftsize value as fragment length in
the later analysis. --off-auto can turn off this default behavior.
** Redundant tag filtering
The IO module is rewritten. The redundant tag filtering process
becomes simpler and works as promise. The maximum allowed number
of tags at the exact same location is calculated from the
sequencing depth and genome size using a binomial distribution,
for both TREAMENT and CONTROL separately. ( previously only
TREATMENT is considered ) The exact same location means the same
coordination and the same strand. Then MACS will only keep at most
this number of tags at the exact same location in the following
analysis. An option --keep-dup can let MACS skip the filtering and
keep all the tags. However this may bring in a lot of sequencing
bias, so you may get many false positive peaks.
** Single wiggle mode
First thing to mention, this is not the score track that I
described before. By default, MACS generates wiggle files for
fragment pileup for every chromosomes separately. When you use
--single-wig option, MACS will generate a single wiggle file for
all the chromosomes so you will get a wig.gz for TREATMENT and
another wig.gz for CONTROL if available.
** Sniff -- automatic format detection
Now, by default or "-f AUTO", MACS will decide the input file
format automatically. Technically, it will try to read at most
1000 records for the first 10 non-comment lines. If it succeeds,
the format is decided. I recommend not to use AUTO and specify the
right format for your input files, unless you combine different
formats in a single MACS run.
* Options changes
--single-wig and --keep-dup are added. Check previous section in
ChangeLog for detail.
-f (--format) AUTO is now the default option.
--slocal default: 1000
--llocal default: 10000
* Bug fixed
Setup script will stop the installation if python version is not
python2.6 or python2.7.
Local lambda calculation has been changed back. MACS will check
peak_region, slocal( default 1K) and llocal (default 10K) for the
local bias. The previous 200bps default will cause MACS misses
some peaks where the input bias is very sharp.
sam2bed.py script is corrected.
Relative pos in xls output is fixed.
Parser for ELAND_export is fixed to pass some of the no match
lines. And elandexport2bed.py is fixed too. ( however I can't
guarantee that it works on any eland_export files. )
2010-06-04 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.4.0alpha2 (be smarter)
* Options changes
--gsize now provides shortcuts for common genomes, including
human, mouse, C. elegans and fruitfly.
--llocal now will be 5000 bps if there is no input file, so that
local lambda doesn't overkill enriched binding sites.
2010-06-02 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.4alpha (be smarter)
* Options changes
--tsize option is redesigned. MACS will use the first 10 lines of
the input to decide the tag size. If user specifies --tsize, it
will override the auto decided tsize.
--lambdaset is replaced by --slocal and --llocal which mean the
small local region and large local region.
--bw has no effect on the scan-window size now. It only affects the
paired-peaks model process.
* Model building
During the model building, MACS will pick out the enriched regions
which are not too high and not too low to build the paired-peak
model. Default the region is from fold 10 to fold 30. If MACS
fails to build the model, by default it will use the nomodel
settings, like shiftsize=100bps, to shift and extend each
tags. This behavior can be turned off by '--off-auto'.
* Output files
An extra file including all the summit positions are saved in
*_summits.bed file. An option '--call-subpeaks' will invoke
PeakSplitter developed by Mali Salmon to split wide peaks into
smaller subpeaks.
* Sniff ( will in beta )
Automatically recognize the input file format, so use can combine
different format in one MACS run.
Not implemented features/TODO:
* Algorithms ( in near future? )
MACS will try to refine the peak boundaries by calculating the
scores for every point in the candidate peak regions. The score
will be the -10*log(10,pvalue) on a local poisson distribution. A
cutoff specified by users (--pvalue) will be applied to find the
precise sub-peaks in the original candidate peak region. Peak
boudaries and peak summits positions will be saved in separate BED
files.
* Single wiggle track ( in near future? )
A single wiggle track will be generated to save the scores within
candidate peak regions in the 10bps resolution. The wiggle file
is in fixedStep format.
2009-10-16 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.7.1 (Oktoberfest, bug fixed #1)
* bin/Constants.py
Fixed typo. FCSTEP -> FESTEP
* lib/PeakDetect.py
The 'femax' attribute bug is fixed
2009-10-02 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.7 (Oktoberfest)
* bin/macs, lib/PeakDetect.py, lib/IO/__init__.py, lib/OptValidator.py
Enhancements by Peter Chines:
1. gzip files are supported.
2. when --diag is on, user can set the increment and endpoint for
fold enrichment analysis by setting --fe-step and --fe-max.
Enhancements by Davide Cittaro:
1. BAM and SAM formats are supported.
2. small changes in the header lines of wiggle output.
Enhancements by Me:
1. I added --fe-min option;
2. Bowtie ascii output with suffix ".map" is supported.
Bug fixed:
1. --nolambda bug is fixed. ( reported by Martin in JHU )
2. --diag bug is fixed. ( reported by Bogdan Tanasa )
3. Function to remove suffix '.fa' is fixed. ( reported by Jeff Johnston )
4. Some "fold change" have been changed to "fold enrichment".
2009-06-10 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.6.1 (default parameter change)
* bin/macs, lib/PeakDetect.py
"--oldfdr" is removed. The 'oldfdr' behaviour becomes
default. "--futurefdr" is added which can turn on the 'new' method
introduced in 1.3.6. By default it's off.
* lib/PeakDetect.py
Fixed a bug. p-value is corrected a little bit.
2009-05-11 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.6 (Birthday cake)
* bin/macs
"track name" is added to the header of BED output file.
Now the default peak detection method is to consider 5k and 10k
nearby regions in treatment data and peak location, 1k, 5k, and
10k regions in control data to calculate local bias. The old
method can be called through '--old' option.
Information about how many total/unique tags in treatment or
control will be saved in final .xls output.
* lib/IO/__init__.py
".fa" will be removed from input tag alignment so only the
chromosome names are kept.
WigTrackI class is added for Wiggle like data structure. (not used
now)
The parser for ELAND multi PET files has been fixed. Now the 5'
tag position for a pair will be kept, whereas in the previous
version, the middle points are kept.
* lib/IO/BinKeeper.py
BinKeeperI class is inspired by Jim Kent's library for UCSC genome
browser, which can quickly access certain region for values in a
large wiggle like data file. (not used now)
* lib/OptValidator.py
typo fixed.
* lib/PeakDetect.py
Now the default peak detection method is to consider 5k and 10k
nearby regions in treatment data and peak location, 1k, 5k, and
10k regions in control data to calculate local bias. The old
method can be called through '--old' option.
Two columns have beed added to BED output file. 4th column: peak
name; 5th column: peak score using -10log(10,pvalue) as score.
* setup.py
Add support to build a Mac App through 'setup.py py2app', or a
Windows executable through 'setup.py py2exe'. You need to install
py2app or py2exe package in order to use these functions.
2009-02-12 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.5 (local lambda fixed, typo fixed, model figure improved)
* PeakDetect.py
Now, besides 1k, 5k, 10k, MACS will also consider peak size region
in control data to calculate local lambda for each peak. Peak
calling results will be slightly different with previous version,
beware!
* OptValidator.py
Typo fixed, ELANDParser -> ELANDResultParser
* OutputWriter.py
Now, modeled d value will be shown on the model figure.
2009-01-06 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.4 (Happy New Year Version, bug fixed, ELAND multi/PET support)
* macs, IO/__init__.py, PeakDetect.py
Add support for ELAND multi format. Add support for Pair-End
experiment, in this case, 5'end and 3'end ELAND multi format files
are required for treatment or control data. See 00README file for
detail.
Add wigextend option.
Add petdist option for Pair-End Tag experiment, which is the best
distance between 5' and 3' tags.
* PeakDetect.py
Fixed a bug which cause the end positions of every peak region
incorrectly added by 1 bp. ( Thanks Mali Salmon!)
* OutputWriter.py
Fix bugs while generating wiggle files. The start position of
wiggle file is set to 1 instead of 0.
Fix a bug that every 10M bps, signals in the first 'd' range are
lower than actual. ( Thanks Mali Salmon!)
2008-12-03 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.3 (wiggle bugs fixed)
* OutputWriter.py
Fix bugs while generating wiggle files. 1. 'span=' is added to
'variableStep' line; 2. previously, every 10M bps, the coordinates
were wrongly shifted to the right for 'd' basepairs.
* macs, PeakDetect.py
Add an option to save wiggle files on different resolution.
2008-10-02 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.2 (tiny bugs fixed)
* IO/__init__.py
Fix 65536 -> 65535. ( Thank Joon)
* Prob.py
Improved for binomial function with extra large number. Imported
from Cistrome project.
* PeakDetect.py
If treatment channel misses reads in some chromosome included in
control channel, or vice versa, MACS will not exit. (Thank Shaun
Mahony)
Instead, MACS will fake a tag at position -1 when calling
treatment peaks vs control, but will ignore the chromosome while
calling negative peaks.
2008-09-04 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3.1 (tiny bugs fixed version)
* Prob.py
Hyunjin Gene Shin contributed some codes to Prob.py. Now the
binomial functions can tolerate large and small numbers.
* IO/__init__.py
Parsers now split lines in BED/ELAND file using any
whitespaces. 'track' or 'browser' lines will be regarded as
comment lines. A bug fixed when throwing StrandFormatError. The
maximum redundant tag number at a single position can be no less
than 65536.
2008-07-15 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.3 (naming clarification version)
* Naming clarification changes according to our manuscript:
'frag_len' is changed to 'd'.
'fold_change' is changed to 'fold_enrichment'.
Suggest '--bw' parameter to be determined by users from the real
sonication size.
Maximum FDR is 100% in the output file.
And other clarifications in 00README file and the documents on the
website.
* IO/__init__.py
If the redundant tag number at a single position is over 32767,
just remember 32767, instead of raising an overflow exception.
* setup.py
fixed a typo.
* PeakDetect.py
Bug fixed for diagnosis report.
2008-07-10 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.2.2gamma
* Serious bugs fix:
Poisson distribution CDF and inverse CDF functions are
corrected. They can produce right results even for huge lambda
now. So that the p-value and FDR values in the final excel sheet
are corrected.
IO package now can tolerate some rare cases; ELANDParser in IO
package is fixed. (Thank Bogdan)
* Improvement:
Reverse paired peaks in model are rejected. So there will be no
negative 'frag_len'. (Thank Bogdan)
* Features added:
Diagnosis function is completed. Which can output a table file for
users to estimate their sequencing depth.
2008-06-30 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.2
* Probe.py is added!
GSL is totally removed from MACS. Instead, I have implemented the
CDF and inverse CDF for poisson and binomial distribution purely
in python.
* Constants.py is added!
Organize constants used in MACS in the Constants.py file.
* All other files are modified!
Foldchange calculation is modified. Now the foldchange only be
calculated at the peak summit position instead of the whole peak
region. The values will be higher and more robust than before.
Features added:
1. MACS can save wiggle format files containing the tag number at
every 10 bp along the genome. Tags are shifted according to our
model before they are calculated.
2. Model building and local lambda calculation can be skipped with
certain options.
3. A diagnosis report can be generated through '--diag'
option. This report can help you get an assumption about the
sequencing saturation. This funtion is only in beta stage.
4. FDR calculation speed is highly improved.
2008-05-28 Tao Liu <taoliu@jimmy.harvard.edu>
Version 1.1
* TabIO, PeakModel.py ...
Bug fixed to let MACS tolerate some cases while there is no tag on
either plus strand or minus strand.
* setup.py
Check the version of python. If the version is lower than 2.4,
refuse to install with warning.
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