NAME

       macs2_refinepeak - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs2 refinepeak [-h] -b BEDFILE -i IFILE [IFILE ...]

       [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}]
              [-c CUTOFF] [-w WINDOWSIZE] [--verbose VERBOSE] [--outdir OUTDIR] (-o OFILE | --o-prefix OPREFIX)

   optional arguments:
       -h, --help
              show this help message and exit

       -b BEDFILE
              Candidate peak file in BED format. REQUIRED.

       -i IFILE [IFILE ...], --ifile IFILE [IFILE ...]
              ChIP-seq alignment file. If multiple files are given as '-t A B C', then they will all be read and
              combined. Note that pair-end data is not supposed to work with this command. REQUIRED.

       -f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}, --format
       {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}
              Format of tag file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or "SAM" or "BAM" or
              "BOWTIE".  The  default  AUTO  option will let 'macs2 refinepeak' decide which format the file is.
              Please     check     the     definition      in      README      file      if      you      choose
              ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE. DEFAULT: "AUTO"

       -c CUTOFF, --cutoff CUTOFF
              Cutoff DEFAULT: 5

       -w WINDOWSIZE, --window-size WINDOWSIZE
              Scan window size on both side of the summit (default: 100bp)

       --verbose VERBOSE
              Set  verbose  level.  0:  only  show critical message, 1: show additional warning message, 2: show
              process information, 3: show debug messages. If you want to know where are  the  duplicate  reads,
              use 3. DEFAULT:2

       --outdir OUTDIR
              If  specified  all  output  files  will be written to that directory. Default: the current working
              directory

       -o OFILE, --ofile OFILE
              Output file name. Mutually exclusive with --o-prefix.

       --o-prefix OPREFIX
              Output file prefix. Mutually exclusive with -o/--ofile.

macs2_refinepeak 2.1.1.20160309                   February 2018                              MACS2_REFINEPEAK(1)