.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH MACS3 "1" "February 2024" "macs3 3.0.1" "User Commands"
.SH NAME
macs3 \- macs3 \- Model\-based Analysis for ChIP\-Sequencing
.SH DESCRIPTION
usage: macs3 [\-h] [\-\-version]
.IP
{callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak,callvar,hmmratac}
\&...
.PP
macs3 \fB\-\-\fR Model\-based Analysis for ChIP\-Sequencing
.SS "positional arguments:"
.IP
{callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak,callvar,hmmratac}
.TP
callpeak
Main MACS3 Function: Call peaks from alignment
results.
.TP
bdgpeakcall
Call peaks from bedGraph file.
.TP
bdgbroadcall
Call nested broad peaks from bedGraph file.
.TP
bdgcmp
Comparing two signal tracks in bedGraph format.
.TP
bdgopt
Operate the score column of bedGraph file.
.TP
cmbreps
Combine bedGraph files of scores from replicates.
.TP
bdgdiff
Differential peak detection based on paired four
bedGraph files.
.TP
filterdup
Remove duplicate reads, then save in BED/BEDPE format
file.
.TP
predictd
Predict d or fragment size from alignment results. In
case of PE data, report the average insertion/fragment
size from all pairs.
.TP
pileup
Pileup aligned reads (single\-end) or fragments
(paired\-end).
.TP
randsample
Randomly choose a number/percentage of total reads,
then save in BED/BEDPE format file.
.TP
refinepeak
Take raw reads alignment, refine peak summits.
Inspired by SPP.
.TP
callvar
Call variants in given peak regions from the alignment
BAM files.
.TP
hmmratac
Dedicated peak calling based on Hidden Markov Model
for ATAC\-seq data.
.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: macs3 COMMAND \fB\-h\fR