DESCRIPTION
usage: macs2 [-h] [--version]- {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak} ...
macs2 -- Model-based Analysis for ChIP-Sequencing
positional arguments:
- {callpeak,bdgpeakcall,bdgbroadcall,bdgcmp,bdgopt,cmbreps,bdgdiff,filterdup,predictd,pileup,randsample,refinepeak}
- callpeak
- Main MACS2 Function: Call peaks from alignment results.
- bdgpeakcall
- Call peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable.
- bdgbroadcall
- Call broad peaks from bedGraph output. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable.
- bdgcmp
- Deduct noise by comparing two signal tracks in bedGraph. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable.
- bdgopt
- Operations on score column of bedGraph file. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable.
- cmbreps
- Combine BEDGraphs of scores from replicates. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable.
- bdgdiff
- Differential peak detection based on paired four bedgraph files. Note: All regions on the same chromosome in the bedGraph file should be continuous so only bedGraph files from MACS2 are accpetable.
- filterdup
- Remove duplicate reads at the same position, then convert acceptable format to BED format.
- predictd
- Predict d or fragment size from alignment results. *Will NOT filter duplicates*
- pileup
- Pileup aligned reads with a given extension size (fragment size or d in MACS language). Note there will be no step for duplicate reads filtering or sequencing depth scaling, so you may need to do certain pre/postprocessing.
- randsample
- Randomly sample number/percentage of total reads.
- refinepeak
- (Experimental) Take raw reads alignment, refine peak summits and give scores measuring balance of waston/crick tags. Inspired by SPP.
optional arguments:
- -h, --help
- show this help message and exit
- --version
- show program's version number and exit
For command line options of each command, type: macs2 COMMAND -h