macs2

Version:: 2.2.7.1
Category:: bio
Cluster:: Loki

Author / Distributor

https://docs.csc.fi/apps/macs2/

Description

MACS (Model-based Analysis of ChIP-Seq) is an analysis tool for NGS ChIP-Seq data. MACS empirically models the length of the sequenced ChIP fragments and use sit to improve the spatial resolution of predicted binding sites. MACS compares can be used with or without control samples.

Documentation

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/post-processing.
   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

Examples/Usage

List available modules:
```
$ module avail macs2
```
Load the macs2 module:
```
$ module load bio/macs2/2.2.7.1
```
Check the loaded modules:
```
$ module list
```
Unload the macs2 module:
```
$ module unload bio/macs2/2.2.7.1
```

Installation

Source code is obtained from macs2