NAME

       mac3_bdgbroadcall - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs3 bdgbroadcall [-h] -i IFILE [-c CUTOFFPEAK] [-C CUTOFFLINK]

       [-l MINLEN] [-g LVL1MAXGAP] [-G LVL2MAXGAP]
              [--no-trackline]  [--verbose  VERBOSE]  [--outdir  OUTDIR]  (-o  OFILE | --o-prefix
              OPREFIX)

   options:
       -h, --help
              show this help message and exit

       -i IFILE, --ifile IFILE
              MACS score in bedGraph. REQUIRED

       -c CUTOFFPEAK, --cutoff-peak CUTOFFPEAK
              Cutoff for peaks depending on which method you used for score track.  If  the  file
              contains  qvalue scores from MACS3, score 2 means qvalue 0.01. Regions with signals
              lower than cutoff will not be considerred as enriched regions. DEFAULT: 2

       -C CUTOFFLINK, --cutoff-link CUTOFFLINK
              Cutoff for linking regions/low abundance regions depending on which method you used
              for  score  track.  If  the  file  contains qvalue scores from MACS3, score 1 means
              qvalue 0.1, and score 0.3 means qvalue 0.5.  DEFAULT: 1

       -l MINLEN, --min-length MINLEN
              minimum length of peak, better to set it as d value.  DEFAULT: 200

       -g LVL1MAXGAP, --lvl1-max-gap LVL1MAXGAP
              maximum gap between significant peaks, better to set it as tag size. DEFAULT: 30

       -G LVL2MAXGAP, --lvl2-max-gap LVL2MAXGAP
              maximum linking between significant peaks, better to set it as 4 times of d  value.
              DEFAULT: 800

       --no-trackline
              Tells  MACS not to include trackline with bedGraph files. The trackline is required
              by UCSC.

       --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

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

       -o OFILE, --ofile OFILE
              Output file name. Mutually exclusive with --o-prefix.

       --o-prefix OPREFIX
              Output file prefix. Mutually exclusive with -o/--ofile.