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macs2_bdgbroadcall - Online in the Cloud

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PROGRAM:

NAME


macs2_bdgbroadcall - Model-based Analysis for ChIP-Sequencing

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.

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