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#title Model-based Analysis for ChIP-Seq

• About

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 newest version is [[Download][version 1.4.0]] And, the beta testing version is [[Download][version 2.0.3]]

• Author

MACS is written by Yong Zhang and [[http://liulab.dfci.harvard.edu/~taoliu/][Tao Liu]] from Xiaole Shirley Liu's Lab.

• Source Code

[[https://github.com/taoliu/MACS/][On Github]]

• Citation

Our paper has been [[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=18798982%5Bpmid%5D][published]] in Genome Biology. Please cite "Zhang et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol (2008) vol. 9 (9) pp. R137".

• License

This software is distributed under the terms of [[http://liulab.dfci.harvard.edu/MACS/COPYING][Artistic License]].

• Contact

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 [[http://groups.google.com/group/macs-announcement][google group]].