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PROGRAM:

NAME


macs2_bdgopt - Model-based Analysis for ChIP-Sequencing

DESCRIPTION


usage: macs2 bdgopt [-h] -i IFILE [-m {multiply,add,p2q}]

[-p [EXTRAPARAM [EXTRAPARAM ...]]] [--outdir OUTDIR] -o
OFILE

optional arguments:
-h, --help
show this help message and exit

-i IFILE, --ifile IFILE
MACS score in bedGraph. Note: this must be a bedGraph file covering the ENTIRE
genome. REQUIRED

-m {multiply,add,p2q}, --method {multiply,add,p2q}
Method to modify the score column of bedGraph file. Available choices are:
multiply, add or p2q. 1) multiply, the EXTRAPARAM is required and will be
multiplied to the score column. If you intend to divide the score column by X, use
value of 1/X as EXTRAPARAM. 2) add, the EXTRAPARAM is required and will be added to
the score column. If you intend to subtract the score column by X, use value of -X
as EXTRAPARAM. 3) p2q, this will convert p-value scores to q-value scores using
Benjamini-Hochberg process. The EXTRAPARAM is not required. This method assumes
the scores are -log10 p-value from MACS2. Any other types of score will cause
unexpected errors.

-p [EXTRAPARAM [EXTRAPARAM ...]], --extra-param [EXTRAPARAM [EXTRAPARAM ...]]
The extra parameter for METHOD. Check the detail of -m option.

--outdir OUTDIR
If specified all output files will be written to that directory. Default: the
current working directory

-o OFILE, --ofile OFILE
Output BEDGraph filename.

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