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.