NAME

       mac3_bdgopt - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs3 bdgopt [-h] -i IFILE [-m {multiply,add,p2q,max,min}]

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

   options:
       -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,max,min}, --method {multiply,add,p2q,max,min}
              Method to modify the  score  column  of  bedGraph  file.   Available  choices  are:
              multiply,  add,  max, min, 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) max, the EXTRAPARAM is required and will take the
              maximum value between score and the EXTRAPARAM. 4) min, the EXTRAPARAM is  required
              and will take the minimum value between score and the EXTRAPARAM. 5) 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
              MACS3. Any other types of score will cause unexpected errors.

       -p [EXTRAPARAM ...], --extra-param [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.

       --verbose VERBOSE
              Set  verbose  level  of  runtime  message.  0:  only show critical message, 1: show
              additional warning message, 2: show process information, 3:  show  debug  messages.
              DEFAULT:2