NAME

       mac3_bdgpeakcall - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs3 bdgpeakcall [-h] -i IFILE [-c CUTOFF] [-l MINLEN] [-g MAXGAP]

       [--cutoff-analysis]
              [--cutoff-analysis-steps    CUTOFF_ANALYSIS_STEPS]    [--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 CUTOFF, --cutoff CUTOFF
              Cutoff depends on which method you used for  score  track.  If  the  file  contains
              pvalue  scores  from  MACS3,  score 5 means pvalue 1e-5. Regions with signals lower
              than cutoff will not be considerred as enriched regions. DEFAULT: 5

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

       -g MAXGAP, --max-gap MAXGAP
              maximum gap between significant points in a peak, better to set  it  as  tag  size.
              DEFAULT: 30

       --cutoff-analysis
              While  set,  bdgpeakcall  will  analyze number or total length of peaks that can be
              called by different cutoff then output a summary table to help user decide a better
              cutoff. Note, minlen and maxgap may affect the results. DEFAULT: False

       --cutoff-analysis-steps CUTOFF_ANALYSIS_STEPS
              Steps  for performing cutoff analysis. It will be used to decide which cutoff value
              should be included in the final report. Larger the  value,  higher  resolution  the
              cutoff analysis can be. But please note, the final report won't necessarily include
              the same number of cutoff values as specified here since we won't output the cutoff
              that yield zero peak. DEFAULT: 100

       --no-trackline
              Tells  MACS  not to include trackline with bedGraph files. The trackline is used by
              UCSC for the options for display.

       --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.