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
              MACS score in bedGraph. Note: this must be a bedGraph file covering the ENTIRE genome. REQUIRED

       -m, --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, --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
              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

macs3 bdgopt 3.0.2                                 March 2025                                     MAC3_BDGOPT(1)