.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH MACS2 "1" "December 2023" "macs2 2.2.9.1" "User Commands"
.SH NAME
macs2 \- macs2 \- Model\-based Analysis for ChIP\-Sequencing
.SH DESCRIPTION
usage: macs2 [\-h] [\-\-version]
.IP
{callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak}
\&...
.PP
macs2 \fB\-\-\fR Model\-based Analysis for ChIP\-Sequencing
.SS "positional arguments:"
.IP
{callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak}
.TP
callpeak
Main MACS2 Function: Call peaks from alignment
results.
.TP
bdgpeakcall
Call peaks from bedGraph output. Note: All regions on
the same chromosome in the bedGraph file should be
continuous so only bedGraph files from MACS2 are
accpetable.
.TP
bdgbroadcall
Call broad peaks from bedGraph output. Note: All
regions on the same chromosome in the bedGraph file
should be continuous so only bedGraph files from MACS2
are accpetable.
.TP
bdgcmp
Deduct noise by comparing two signal tracks in
bedGraph. Note: All regions on the same chromosome in
the bedGraph file should be continuous so only
bedGraph files from MACS2 are accpetable.
.TP
bdgopt
Operations on score column of bedGraph file. Note: All
regions on the same chromosome in the bedGraph file
should be continuous so only bedGraph files from MACS2
are accpetable.
.TP
cmbreps
Combine BEDGraphs of scores from replicates. Note: All
regions on the same chromosome in the bedGraph file
should be continuous so only bedGraph files from MACS2
are accpetable.
.TP
bdgdiff
Differential peak detection based on paired four
bedgraph files. Note: All regions on the same
chromosome in the bedGraph file should be continuous
so only bedGraph files from MACS2 are accpetable.
.TP
filterdup
Remove duplicate reads at the same position, then save
the rest alignments to BED or BEDPE file. If you use '
\fB\-\-keep\-dup\fR all option', this script can be utilized to
convert any acceptable format into BED or BEDPE
format.
.TP
predictd
Predict d or fragment size from alignment results.
*Will NOT filter duplicates*
.TP
pileup
Pileup aligned reads with a given extension size
(fragment size or d in MACS language). Note there will
be no step for duplicate reads filtering or sequencing
depth scaling, so you may need to do certain pre/postprocessing.
.TP
randsample
Randomly sample number/percentage of total reads.
.TP
refinepeak
(Experimental) Take raw reads alignment, refine peak
summits and give scores measuring balance of
waston/crick tags. Inspired by SPP.
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-version\fR
show program's version number and exit
.PP
For command line options of each command, type: macs2 COMMAND \fB\-h\fR