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.