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.

macs3 bdgpeakcall 3.0.1                            April 2024                                MAC3_BDGPEAKCALL(1)