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.

options:

  -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