table of contents
MAC3_BDGPEAKCALL(1) | User Commands | MAC3_BDGPEAKCALL(1) |
NAME¶
mac3_bdgpeakcall - Model-based Analysis for ChIP-Sequencing
DESCRIPTION¶
usage: macs3 bdgpeakcall [-h] -i IFILE [-c CUTOFF] [-l MINLEN] [-g MAXGAP]
- [--cutoff-analysis]
- [--cutoff-analysis-steps CUTOFF_ANALYSIS_STEPS] [--no-trackline] [--verbose VERBOSE] [--outdir OUTDIR] (-o OFILE | --o-prefix OPREFIX)
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 MACS3, score 5 means pvalue 1e-5. Regions with signals lower than cutoff will not be considerred as enriched regions. 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
- --cutoff-analysis-steps CUTOFF_ANALYSIS_STEPS
- Steps for performing cutoff analysis. It will be used to decide which cutoff value should be included in the final report. Larger the value, higher resolution the cutoff analysis can be. But please note, the final report won't necessarily include the same number of cutoff values as specified here since we won't output the cutoff that yield zero peak. DEFAULT: 100
- --no-trackline
- Tells MACS not to include trackline with bedGraph files. The trackline is used by UCSC for the options for display.
- --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 OFILE
- Output file name. Mutually exclusive with --o-prefix.
- --o-prefix OPREFIX
- Output file prefix. Mutually exclusive with -o/--ofile.
February 2024 | macs3 bdgpeakcall 3.0.1 |