This is the command macs2_bdgopt that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
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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