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.