.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH MACS2_REFINEPEAK "1" "May 2016" "macs2_refinepeak 2.1.1.20160309" "User Commands"
.SH NAME
macs2_refinepeak \- Model\-based Analysis for ChIP\-Sequencing
.SH DESCRIPTION
usage: macs2 refinepeak [\-h] \fB\-b\fR BEDFILE \fB\-i\fR IFILE [IFILE ...]
.TP
[\-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}]
[\-c CUTOFF] [\-w WINDOWSIZE] [\-\-verbose VERBOSE]
[\-\-outdir OUTDIR] (\fB\-o\fR OFILE | \fB\-\-o\-prefix\fR OPREFIX)
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-b\fR BEDFILE
Candidate peak file in BED format. REQUIRED.
.TP
\fB\-i\fR IFILE [IFILE ...], \fB\-\-ifile\fR 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.
.TP
\fB\-f\fR {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}, \fB\-\-format\fR {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"
.TP
\fB\-c\fR CUTOFF, \fB\-\-cutoff\fR CUTOFF
Cutoff DEFAULT: 5
.TP
\fB\-w\fR WINDOWSIZE, \fB\-\-window\-size\fR WINDOWSIZE
Scan window size on both side of the summit (default:
100bp)
.TP
\fB\-\-verbose\fR 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
.TP
\fB\-\-outdir\fR OUTDIR
If specified all output files will be written to that
directory. Default: the current working directory
.TP
\fB\-o\fR OFILE, \fB\-\-ofile\fR OFILE
Output file name. Mutually exclusive with \fB\-\-o\-prefix\fR.
.TP
\fB\-\-o\-prefix\fR OPREFIX
Output file prefix. Mutually exclusive with
\fB\-o\fR/\-\-ofile.