NAME

       macs3 - macs3 - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs3 [-h] [--version]

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

       macs3 -- Model-based Analysis for ChIP-Sequencing

   positional arguments:
              {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak,callvar,hmmratac}

       callpeak
              Main MACS3 Function: Call peaks from alignment results.

       bdgpeakcall
              Call peaks from bedGraph file.

       bdgbroadcall
              Call nested broad peaks from bedGraph file.

       bdgcmp Comparing two signal tracks in bedGraph format.

       bdgopt Operate the score column of bedGraph file.

       cmbreps
              Combine bedGraph files of scores from replicates.

       bdgdiff
              Differential peak detection based on paired four bedGraph files.

       filterdup
              Remove duplicate reads, then save in BED/BEDPE format file.

       predictd
              Predict  d  or  fragment  size  from  alignment  results.  In  case of PE data, report the average
              insertion/fragment size from all pairs.

       pileup Pileup aligned reads (single-end) or fragments (paired-end).

       randsample
              Randomly choose a number/percentage of total reads, then save in BED/BEDPE format file.

       refinepeak
              Take raw reads alignment, refine peak summits.  Inspired by SPP.

       callvar
              Call variants in given peak regions from the alignment BAM files.

       hmmratac
              Dedicated peak calling based on Hidden Markov Model for ATAC-seq data.

   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: macs3 COMMAND -h

macs3 3.0.2                                        March 2025                                           MACS3(1)