Man page - macs3_bdgbroadcall(1)

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Manual

MAC3_BDGBROADCALL

NAME
DESCRIPTION
options:

NAME

mac3_bdgbroadcall - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

usage: macs3 bdgbroadcall [-h] -i IFILE [-c CUTOFFPEAK] [-C CUTOFFLINK]
[-l MINLEN] [-g LVL1MAXGAP] [-G LVL2MAXGAP]

[--no-trackline] [--verbose VERBOSE] [--outdir OUTDIR] ( -o OFILE | --o-prefix OPREFIX)

options:

-h , --help

show this help message and exit

-i , --ifile IFILE

MACS score in bedGraph. REQUIRED

-c , --cutoff-peak CUTOFFPEAK

Cutoff for peaks depending on which method you used for score track. If the file contains qvalue scores from MACS3, score 2 means qvalue 0.01. Regions with signals lower than cutoff will not be considerred as enriched regions. DEFAULT: 2

-C , --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 MACS3, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. DEFAULT: 1

-l , --min-length MINLEN

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

-g , --lvl1-max-gap LVL1MAXGAP

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

-G , --lvl2-max-gap LVL2MAXGAP

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

--no-trackline

Tells MACS not to include trackline with bedGraph files. The trackline is required by UCSC.

--verbose VERBOSE

Set verbose level of runtime message. 0: only show critical message, 1: show additional warning message, 2: show process information, 3: show debug messages. DEFAULT:2

--outdir OUTDIR

If specified all output files will be written to that directory. Default: the current working directory

-o , --ofile OFILE

Output file name. Mutually exclusive with --o-prefix .

--o-prefix OPREFIX

Output file prefix. Mutually exclusive with -o /--ofile.