macs2_refinepeak(1)
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.