MACS3

usage: macs2 [-h] [--version]
             {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak}
             ...

macs2 -- Model-based Analysis for ChIP-Sequencing

positional arguments:
  {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak}
    callpeak            Main MACS2 Function: Call peaks from alignment
                        results.
    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.
    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.
    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.
    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.
    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.
    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.
    filterdup           Remove duplicate reads at the same position, then save
                        the rest alignments to BED or BEDPE file. If you use
                        '--keep-dup all option', this script can be utilized
                        to convert any acceptable format into BED or BEDPE
                        format.
    predictd            Predict d or fragment size from alignment results.
                        *Will NOT filter duplicates*
    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/post-
                        processing.
    randsample          Randomly sample number/percentage of total reads.
    refinepeak          (Experimental) Take raw reads alignment, refine peak
                        summits and give scores measuring balance of
                        waston/crick tags. Inspired by SPP.

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

For command line options of each command, type: macs2 COMMAND -h