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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.


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


Version on CSC's Servers

  • Puhti:, 3.0.0a7
  • Chipster graphical user interface


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

module load macs

Module macs/ also loads MACS 3.0.0a7.

After that you can start MACS with command:

macs2 -h
macs3 -h

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

More information

Last update: October 10, 2022