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-max    CUTOFF_ANALYSIS_MAX]   [--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
              MACS score in bedGraph. REQUIRED

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

       -g, --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-max CUTOFF_ANALYSIS_MAX
              The  maximum  cutoff  score for performing cutoff analysis. Together with --cutoff-analysis-steps,
              the resolution  in  the  final  report  can  be  controlled.   Please  check  the  description  in
              --cutoff-analysissteps for detail. DEFAULT: 100

       --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.  The
              cutoff  analysis function will first find the smallest (at least 0) and the largest (controlled by
              --cutoff-analysis-max)   score   in   the   data,   then   break   the   range   of   score   into
              `CUTOFF_ANALYSIS_STEPS`  intervals.  It  will  then  use  each  score  as cutoff to call peaks and
              calculate the total number of candidate peaks, the total  basepairs  of  peaks,  and  the  average
              length  of  peak  in  basepair.   Please  note  that  the  final  report  ideally  should  include
              `CUTOFF_ANALYSIS_STEPS` rows, but in practice, if the cutoff yield zero peak,  the  row  for  that
              value won't be included. 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
              Output file name. Mutually exclusive with --o-prefix.

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

macs3 bdgpeakcall 3.0.2                            March 2025                                MAC3_BDGPEAKCALL(1)