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

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