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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 on short reads sequencers such as Genome Analyzer (Illumina / Solexa). 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. Also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. 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 Author is written by Yong Zhang and from Xiaole Shirley Liu's Lab. Source Code Citation Our paper has been in Genome Biology.
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Please cite 'Zhang et al. Model-based Analysis of ChIP-Seq. Genome Biol (2008) vol. License This software is distributed under the terms of. Contact If you have any comments, suggestions, questions, bug reports, etc, feel free to contact: macs dot supporter at gmail.
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