.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH MAC3_BDGPEAKCALL "1" "February 2024" "macs3 bdgpeakcall 3.0.1" "User Commands"
.SH NAME
mac3_bdgpeakcall \- Model\-based Analysis for ChIP\-Sequencing
.SH DESCRIPTION
usage: macs3 bdgpeakcall [\-h] \fB\-i\fR IFILE [\-c CUTOFF] [\-l MINLEN] [\-g MAXGAP]
.TP
[\-\-cutoff\-analysis]
[\-\-cutoff\-analysis\-steps CUTOFF_ANALYSIS_STEPS]
[\-\-no\-trackline] [\-\-verbose VERBOSE]
[\-\-outdir OUTDIR] (\fB\-o\fR OFILE | \fB\-\-o\-prefix\fR OPREFIX)
.SS "options:"
.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 MACS3,
score 5 means pvalue 1e\-5. Regions with signals lower
than cutoff will not be considerred as enriched
regions. 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\-\-cutoff\-analysis\-steps\fR CUTOFF_ANALYSIS_STEPS
Steps for performing cutoff analysis. It will be used
to decide which cutoff value should be included in the
final report. Larger the value, higher resolution the
cutoff analysis can be. But please note, the final
report won't necessarily include the same number of
cutoff values as specified here since we won't output
the cutoff that yield zero peak. DEFAULT: 100
.TP
\fB\-\-no\-trackline\fR
Tells MACS not to include trackline with bedGraph
files. The trackline is used by UCSC for the options
for display.
.TP
\fB\-\-verbose\fR VERBOSE
Set verbose level of runtime message. 0: only show
critical message, 1: show additional warning message,
2: show process information, 3: show debug messages.
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.