.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH MACS2_BDGBROADCALL "1" "December 2020" "macs2 bdgbroadcall 2.2.7.1" "User Commands"
.SH NAME
macs2_bdgbroadcall \- Model\-based Analysis for ChIP\-Sequencing
.SH DESCRIPTION
usage: macs2 bdgbroadcall [\-h] \fB\-i\fR IFILE [\-c CUTOFFPEAK] [\-C CUTOFFLINK]
.TP
[\-l MINLEN] [\-g LVL1MAXGAP] [\-G LVL2MAXGAP]
[\-\-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 CUTOFFPEAK, \fB\-\-cutoff\-peak\fR CUTOFFPEAK
Cutoff for peaks depending on which method you used
for score track. If the file contains qvalue scores
from MACS2, score 2 means qvalue 0.01. DEFAULT: 2
.TP
\fB\-C\fR CUTOFFLINK, \fB\-\-cutoff\-link\fR CUTOFFLINK
Cutoff for linking regions/low abundance regions
depending on which method you used for score track. If
the file contains qvalue scores from MACS2, score 1
means qvalue 0.1, and score 0.3 means qvalue 0.5.
DEFAULT: 1
.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 LVL1MAXGAP, \fB\-\-lvl1\-max\-gap\fR LVL1MAXGAP
maximum gap between significant peaks, better to set
it as tag size. DEFAULT: 30
.TP
\fB\-G\fR LVL2MAXGAP, \fB\-\-lvl2\-max\-gap\fR LVL2MAXGAP
maximum linking between significant peaks, better to
set it as 4 times of d value. DEFAULT: 800
.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.