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macs2_bdgpeakcall - Model-based Analysis for ChIP-Sequencing


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

[--cutoff-analysis] [--no-trackline]
[--outdir OUTDIR] (-o OFILE | --o-prefix OPREFIX)

optional arguments:
-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.

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

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.

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