NAME
macs2 - macs2 - Model-based Analysis for ChIP-Sequencing
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 save the rest alignments to BED or BEDPE file. If you use ' --keep-dup all option', this script can be utilized to convert any acceptable format into BED or BEDPE 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.
options:
- -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