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] [--buffer-size BUFFER_SIZE] [--verbose VERBOSE] [--outdir OUTDIR] (-o
              OFILE | --o-prefix OPREFIX)

   options:
       -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)

       --buffer-size BUFFER_SIZE
              Buffer size for incrementally increasing internal array size to store reads alignment information.
              In most cases, you don't have to change this parameter.  However, if there  are  large  number  of
              chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size
              in order to decrease memory usage (but it will take longer time to read alignment files).  Minimum
              memory  requested  for reading an alignment file is about # of CHROMOSOME * BUFFER_SIZE * 8 Bytes.
              DEFAULT: 100000

       --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.