.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH MACS2_BDGCMP "1" "December 2023" "macs2 bdgcmp 2.2.9.1" "User Commands"
.SH NAME
macs2_bdgcmp \- Model\-based Analysis for ChIP\-Sequencing
.SH DESCRIPTION
usage: macs2 bdgcmp [\-h] \fB\-t\fR TFILE \fB\-c\fR CFILE [\-S SFACTOR] [\-p PSEUDOCOUNT]
.TP
[\-m {ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} [{ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} ...]]
[\-\-outdir OUTDIR]
(\fB\-\-o\-prefix\fR OPREFIX | \fB\-o\fR OFILE [OFILE ...])
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-t\fR TFILE, \fB\-\-tfile\fR TFILE
Treatment bedGraph file, e.g. *_treat_pileup.bdg from
MACSv2. REQUIRED
.TP
\fB\-c\fR CFILE, \fB\-\-cfile\fR CFILE
Control bedGraph file, e.g. *_control_lambda.bdg from
MACSv2. REQUIRED
.TP
\fB\-S\fR SFACTOR, \fB\-\-scaling\-factor\fR SFACTOR
Scaling factor for treatment and control track. Keep
it as 1.0 or default in most cases. Set it ONLY while
you have SPMR output from MACS2 callpeak, and plan to
calculate scores as MACS2 callpeak module. If you want
to simulate 'callpeak' w/o '\-\-to\-large', calculate
effective smaller sample size after filtering redudant
reads in million (e.g., put 31.415926 if effective
reads are 31,415,926) and input it for '\-S'; for
\&'callpeak \fB\-\-to\-large\fR', calculate effective reads in
larger sample. DEFAULT: 1.0
.TP
\fB\-p\fR PSEUDOCOUNT, \fB\-\-pseudocount\fR PSEUDOCOUNT
The pseudocount used for calculating logLR, logFE or
FE. The count will be applied after normalization of
sequencing depth. DEFAULT: 0.0, no pseudocount is
applied.
.TP
\fB\-m\fR {ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} [{ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} ...], \fB\-\-method\fR {ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} [{ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} ...]
Method to use while calculating a score in any bin by
comparing treatment value and control value. Available
choices are: ppois, qpois, subtract, logFE, logLR, and
slogLR. They represent Poisson Pvalue (\fB\-log10\fR(pvalue)
form) using control as lambda and treatment as
observation, q\-value through a BH process for poisson
pvalues, subtraction from treatment, linear scale fold
enrichment, log10 fold enrichment(need to set
pseudocount), log10 likelihood between ChIP\-enriched
model and open chromatin model(need to set
pseudocount), symmetric log10 likelihood between two
ChIP\-enrichment models, or maximum value between the
two tracks. Default option is ppois.
.TP
\fB\-\-outdir\fR OUTDIR
If specified all output files will be written to that
directory. Default: the current working directory
.TP
\fB\-\-o\-prefix\fR OPREFIX
The PREFIX of output bedGraph file to write scores. If
it is given as A, and method is 'ppois', output file
will be A_ppois.bdg. Mutually exclusive with
\fB\-o\fR/\-\-ofile.
.TP
\fB\-o\fR OFILE [OFILE ...], \fB\-\-ofile\fR OFILE [OFILE ...]
Output filename. Mutually exclusive with \fB\-\-o\-prefix\fR.
The number and the order of arguments for \fB\-\-ofile\fR must
be the same as for \fB\-m\fR.