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