-
Notifications
You must be signed in to change notification settings - Fork 269
Home
- How to Build Signal Track
- How to call broader peaks
- How to Deal With Pair-end data
- How to Improve resolution
Next generation parallel sequencing technologies made chromatin immunoprecipitation followed by sequencing (ChIP-Seq) a popular strategy to study genome-wide protein-DNA interactions, while creating challenges for analysis algorithms. We present Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, 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 favorably to existing ChIP-Seq peak-finding algorithms, is publicly available open source, and can be used for ChIP-Seq with or without control samples.
Now, the stable version is version 1.4.1
And, the stable release of MACS2 is version 2.0.10. You can check out developing codes from Github
First version MACS was written by Yong Zhang and Tao Liu from Xiaole Shirley Liu's Lab. And Now Tao Liu is the main developer. Ben Schiller helped with differential calling module and pair-end sequencing support. Many users of MACS community contribute their patches.
https://github.com/taoliu/MACS/
Our paper has been published in Genome Biology. Please cite "Zhang et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol (2008) vol. 9 (9) pp. R137".
This software is distributed under the terms of Artistic License. I am considering using a more relaxed open-source license in the future.
If you have any comments, suggestions, questions, bug reports, etc, feel free to contact: macs dot supporter at gmail. And PLEASE attach your command line and log messages if possible.
If you think your question/comment may be interesting to the MACS user group, please post it to our google group.