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.

macs3 refinepeak 3.0.1                             April 2024                                 MAC3_REFINEPEAK(1)