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MACS2/3

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 uses it to improve the spatial resolution of predicted binding sites.

MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. MACS can be used for ChIP-Seq with or without control samples.

License

Free to use and open source under BSD 3-Clause License.

Available

  • Roihu-CPU: 2.2.9.1, 3.0.4
  • Chipster graphical user interface

Usage

To check installed version on Roihu run command:

module spider macs

To set up MACS2 or MACS3 commands in Roihu, give command:

module load macs/<version>

For example

After that you can start MACS with command:

module load macs/2.2.9.1
macs2 -h

or

module load macs/3.0.4
macs3 -h

Short MACS jobs can be executed as interactive batch jobs in Roihu. Longer jobs should be run as batch jobs.

More information