NAME

       mac3_refinepeak - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs3 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  'macs3  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. Regions with SPP wtd score lower  than  cutoff  will  not  be  considerred.
              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.