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.