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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: 2.2.6 Chipster graphical user interface


To set up MACS2 commands in puhti, give command:

module load bioconda

After that you can start MACS2 with command:

macs2 -h

Larger MACS jobs should be executed as a batch job in Puhti. Puhti User Guide for more information on running batch jobs.

More information

Last update: March 29, 2021