.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH MACS2_BDGPEAKCALL "1" "December 2020" "macs2 bdgpeakcall 2.2.7.1" "User Commands"
.SH NAME
macs2_bdgpeakcall \- Model\-based Analysis for ChIP\-Sequencing
.SH DESCRIPTION
usage: macs2 bdgpeakcall [\-h] \fB\-i\fR IFILE [\-c CUTOFF] [\-l MINLEN] [\-g MAXGAP]
.TP
[\-\-cutoff\-analysis] [\-\-no\-trackline]
[\-\-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\-i\fR IFILE, \fB\-\-ifile\fR IFILE
MACS score in bedGraph. REQUIRED
.TP
\fB\-c\fR CUTOFF, \fB\-\-cutoff\fR CUTOFF
Cutoff depends on which method you used for score
track. If the file contains pvalue scores from MACS2,
score 5 means pvalue 1e\-5. DEFAULT: 5
.TP
\fB\-l\fR MINLEN, \fB\-\-min\-length\fR MINLEN
minimum length of peak, better to set it as d value.
DEFAULT: 200
.TP
\fB\-g\fR MAXGAP, \fB\-\-max\-gap\fR MAXGAP
maximum gap between significant points in a peak,
better to set it as tag size. DEFAULT: 30
.TP
\fB\-\-cutoff\-analysis\fR
While set, bdgpeakcall will analyze number or total
length of peaks that can be called by different cutoff
then output a summary table to help user decide a
better cutoff. Note, minlen and maxgap may affect the
results. DEFAULT: False
.TP
\fB\-\-no\-trackline\fR
Tells MACS not to include trackline with bedGraph
files. The trackline is required by UCSC.
.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.