Galaxy |

MACS2.1.2 (version 2.1.2-galaxy1)

Experiment Name:

Type of region to call:

Broad regions are formed by linking nearby enriched regions

Format of input read data:

Specify the format of the input data and whether or not it is paired end (--format)

ChIP-seq read file:

ChIP-seq control read file:

Effective genome size:

Either pre-defined (for common organisms), or user-defined (--gsize)

Band width:

(--bw)

Include XLS file from MACS:

MACS2 XLS file will be output to the history in 'interval' format (suitable for subsequent analysis in Galaxy). Note that start positions are 1-based.

Save treatment and control lambda pileups in bedGraph:

Select p-value or q-value:

default uses q-value

q-value cutoff for binding region detection:

default: 0.01 (--qvalue)

Use advanced options?:

Build Model:

What it does

MACS (Model-based Analysis of ChIP-seq) 2.1.2 provides algorithms for identifying transcript factor binding sites. The program can be used either for ChIP-Seq data alone, or with control sample data to improve specificity.

View the MACS2 documentation at: https://github.com/taoliu/MACS/blob/master/README.rst

Usage

The tool interfaces with the callpeak function in MACS, which calls peaks from alignment results.

Credits

This Galaxy tool was based on the MACS2 tool hosted in the Galaxy toolshed at

http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2

(specifically the 16:14f378e35191 revision of the tool) which is credited to Ziru Zhou. This version is a reimplemented version developed within the Bioinformatics Core Facility at the University of Manchester, which uses more up-to-date Galaxy syntax and adds some extra features.

The tool runs Tao Liu's MACS2 software:

https://github.com/taoliu/MACS

The reference for MACS is:

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.

Please kindly acknowledge both this Galaxy tool and the MACS2 package if you use it.