NEXT-peak: a normal-exponential two-peak model for peak-calling in ChIP-seq data.

ABSTRACT:

Background

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) can locate transcription factor binding sites on genomic scale. Although many models and programs are available to call peaks, none has dominated its competition in comparison studies.

Results

We propose a rigorous statistical model, the normal-exponential two-peak (NEXT-peak) model, which parallels the physical processes generating the empirical data, and which can naturally incorporate mappability information. The model therefore estimates total strength of binding (even if some binding locations do not map uniquely into a reference genome, effectively censoring them); it also assigns an error to an estimated binding location. The comparison study with existing programs on real ChIP-

SUBMITTER: Kim NK 

PROVIDER: S-EPMC3672025 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature