macs2 - Online in the Cloud

PROGRAM:

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 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

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