DESCRIPTION

usage: macs2 bdgbroadcall [-h] -i IFILE [-c CUTOFFPEAK] [-C CUTOFFLINK]

[-l MINLEN] [-g LVL1MAXGAP] [-G LVL2MAXGAP]

[--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 CUTOFFPEAK, --cutoff-peak CUTOFFPEAK

Cutoff for peaks depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 2 means qvalue 0.01. DEFAULT: 2

-C CUTOFFLINK, --cutoff-link CUTOFFLINK

Cutoff for linking regions/low abundance regions depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. DEFAULT: 1

-l MINLEN, --min-length MINLEN

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

-g LVL1MAXGAP, --lvl1-max-gap LVL1MAXGAP

maximum gap between significant peaks, better to set it as tag size. DEFAULT: 30

-G LVL2MAXGAP, --lvl2-max-gap LVL2MAXGAP

maximum linking between significant peaks, better to set it as 4 times of d value. DEFAULT: 800

--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.