macs2 - macs2 - Model-based Analysis for ChIP-Sequencing

       usage: macs2 [-h] [--version]

              {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak}
              ...

       macs2 -- Model-based Analysis for ChIP-Sequencing

   positionalarguments:
              {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/postprocessing.

       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

macs2 2.2.7.1                                      April 2022                                           MACS2(1)

       macs2 - macs2 - Model-based Analysis for ChIP-Sequencing