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macs2_bdgcmp - Model-based Analysis for ChIP-Sequencing


usage: macs2 bdgcmp [-h] -t TFILE -c CFILE [-S SFACTOR] [-p PSEUDOCOUNT]

[-m {ppois,qpois,subtract,logFE,FE,logLR,slogLR}
[{ppois,qpois,subtract,logFE,FE,logLR,slogLR} ...]]
[--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.

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}
[{ppois,qpois,subtract,logFE,FE,logLR,slogLR} ...], --method
{ppois,qpois,subtract,logFE,FE,logLR,slogLR} [{ppois,qpois,subtract,logFE,FE,logLR,slogLR}
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), and symmetric log10 likelihood
between two ChIP-enrichment models. 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.

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