https://github.com/poisonalien/callpeaks
Bash script to call peaks from MACS2 peak caller
https://github.com/poisonalien/callpeaks
Last synced: about 1 year ago
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Bash script to call peaks from MACS2 peak caller
- Host: GitHub
- URL: https://github.com/poisonalien/callpeaks
- Owner: PoisonAlien
- Created: 2021-03-15T15:15:15.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2021-03-15T15:16:53.000Z (about 5 years ago)
- Last Synced: 2025-02-05T16:48:55.734Z (over 1 year ago)
- Language: Shell
- Size: 3.91 KB
- Stars: 2
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# callpeaks
Bash script to call peaks from MACS2 peak caller
```
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usage: callpeaks [options]
callpeaks - wrapper around macs2 callpeak. Also generates bigWigs from bedGraphs by subtracting input signal.
positional arguments:
ChIP bam file. Required.
optional arguments:
-d Output directory to store results. Optional. Default ./macs_op
-o Basename for output file. Usually sample name. Default parses from
-f Format of Input file, AUTO, BED or ELAND or ELANDMULTI or ELANDEXPORT or SAM or BAM or BOWTIE or BAMPE or BEDPE
-g Effective genome size. Default hs. (can be mm, ce, dm)
-q Minimum FDR (q-value) cutoff for peak detection. Deafult 0.05
-i Input bam file. e.g, IgG or whole cell extract
-b Call broad peaks. Default false
Broad histone marks: H3F3A H3K27me3 H3K4me1 H3K79me2 H3K79me3 H3K9me1 H3K9me2 H4K20me1
Narrow histone marks: H2AFZ H3ac H3K27ac H3K4me2 H3K4me3 H3K9ac
See here: https://www.encodeproject.org/chip-seq/histone/
Example: callpeaks -i HeLa_IgG.bam HeLa_H3K27Ac.bam
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```