NAME

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

DESCRIPTION

       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/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