A Generalized Linear Model for Peak Calling in ChIP-Seq Data

Résumé du livre

Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) has become a routine for detecting genome-wide protein-DNA interaction. The success of ChIP- Seq data analysis highly depends on the quality of peak calling to detect peaks of tag counts at a genomic location and evaluate if the peak corresponds to a real protein-DNA interaction event. The challenges in peak calling include 1) how to combine the forward and the reverse strand tag data to improve the power of peak calling, 2) how to account for the variation of tag data observed across different genomic locations, and 3) how to use the negative control data to reduce false positives caused by regional biases that might be generated by local structure.