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.

macs3 bdgbroadcall 3.0.1                           April 2024                               MAC3_BDGBROADCALL(1)