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.