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Warning!

Puhti and Mahti will be decommissioned after Roihu becomes available. Users should clean up unnecessary files and move any required data by the end of August 2026. See the Roihu data preparation instructions for details.

Puhti scratch is very full: keep only active data there and move or delete everything else. No new Puhti scratch quota will be granted.

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 compares can be used for ChIP-Seq with or without control samples.

License

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

Available

  • Puhti: 2.2.7.1, 3.0.0a7, 3.0.1
  • Chipster graphical user interface

Usage

To check installed version on Puhti run command:

module spider macs

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

module load macs/<version>

For example

After that you can start MACS with command:

module load macs/2.2.7.1
macs2 -h

or

module load macs/3.0.1
macs3 -h

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

More information