NAME

       macs2_bdgpeakcall - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs2 bdgpeakcall [-h] -i IFILE [-c CUTOFF] [-l MINLEN] [-g MAXGAP]

       [--cutoff-analysis] [--no-trackline]
              [--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 MACS2, score 5 means pvalue 1e-5. 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

       --no-trackline
              Tells  MACS not to include trackline with bedGraph files. The trackline is required
              by UCSC.

       --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.