macs2_bdgcmp(1)
Modelbased Analysis for ChIPSequencing
DESCRIPTION
usage: macs2 bdgcmp [h]
t TFILE
c CFILE [S SFACTOR] [p PSEUDOCOUNT]
 [m {ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} [{ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} ...]]

[outdir OUTDIR]
(oprefix OPREFIX  o OFILE [OFILE ...])
optional arguments:
 h, help

show this help message and exit
 t TFILE, tfile TFILE

Treatment bedGraph file, e.g. *_treat_pileup.bdg from
MACSv2. REQUIRED
 c CFILE, cfile CFILE

Control bedGraph file, e.g. *_control_lambda.bdg from
MACSv2. REQUIRED
 S SFACTOR, scalingfactor 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 'tolarge', 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 tolarge', calculate effective reads in
larger sample. DEFAULT: 1.0
 p PSEUDOCOUNT, pseudocount 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.
 m {ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} [{ppois,qpois,subtract,logFE,FE,logLR,slogLR,max} ...], method {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 (log10(pvalue)
form) using control as lambda and treatment as
observation, qvalue through a BH process for poisson
pvalues, subtraction from treatment, linear scale fold
enrichment, log10 fold enrichment(need to set
pseudocount), log10 likelihood between ChIPenriched
model and open chromatin model(need to set
pseudocount), symmetric log10 likelihood between two
ChIPenrichment models, or maximum value between the
two tracks. Default option is ppois.
 outdir OUTDIR

If specified all output files will be written to that
directory. Default: the current working directory
 oprefix 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
o/ofile.
 o OFILE [OFILE ...], ofile OFILE [OFILE ...]

Output filename. Mutually exclusive with oprefix.
The number and the order of arguments for ofile must
be the same as for m.