Provided by: macs_2.1.1.20160309-2_amd64 
NAME
macs2_bdgcmp - Model-based Analysis for ChIP-Sequencing
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] (--o-prefix 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, --scaling-factor 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 --to-large', 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, 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.
--outdir OUTDIR
If specified all output files will be written to that directory. Default: the current working
directory
--o-prefix 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 --o-prefix. The number and the order of arguments for
--ofile must be the same as for -m.