.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH MAC3_BDGCMP "1" "February 2024" "macs3 bdgcmp 3.0.1" "User Commands"
.SH NAME
mac3_bdgcmp \- Model\-based Analysis for ChIP\-Sequencing
.SH DESCRIPTION
usage: macs3 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} ...]]
[\-\-verbose VERBOSE] [\-\-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 MACS3 callpeak, and plan to
calculate scores as MACS3 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, FE, logLR,
slogLR, and max. 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\-\-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\-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.