.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH MAC3_BDGOPT "1" "February 2024" "macs3 bdgopt 3.0.1" "User Commands"
.SH NAME
mac3_bdgopt \- Model\-based Analysis for ChIP\-Sequencing
.SH DESCRIPTION
usage: macs3 bdgopt [\-h] \fB\-i\fR IFILE [\-m {multiply,add,p2q,max,min}]
.TP
[\-p [EXTRAPARAM ...]] [\-\-outdir OUTDIR] \fB\-o\fR OFILE
[\-\-verbose VERBOSE]
.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. Note: this must be a bedGraph
file covering the ENTIRE genome. REQUIRED
.TP
\fB\-m\fR {multiply,add,p2q,max,min}, \fB\-\-method\fR {multiply,add,p2q,max,min}
Method to modify the score column of bedGraph file.
Available choices are: multiply, add, max, min, or
p2q. 1) multiply, the EXTRAPARAM is required and will
be multiplied to the score column. If you intend to
divide the score column by X, use value of 1/X as
EXTRAPARAM. 2) add, the EXTRAPARAM is required and
will be added to the score column. If you intend to
subtract the score column by X, use value of \fB\-X\fR as
EXTRAPARAM. 3) max, the EXTRAPARAM is required and
will take the maximum value between score and the
EXTRAPARAM. 4) min, the EXTRAPARAM is required and
will take the minimum value between score and the
EXTRAPARAM. 5) p2q, this will convert p\-value scores
to q\-value scores using Benjamini\-Hochberg process.
The EXTRAPARAM is not required. This method assumes
the scores are \fB\-log10\fR p\-value from MACS3. Any other
types of score will cause unexpected errors.
.TP
\fB\-p\fR [EXTRAPARAM ...], \fB\-\-extra\-param\fR [EXTRAPARAM ...]
The extra parameter for METHOD. Check the detail of \fB\-m\fR
option.
.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 BEDGraph filename.
.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