HistoneHMM: Differential analysis of histone modifications with broad genomic footprints.

ABSTRACT:

Background

ChIP-seq has become a routine method for interrogating the genome-wide distribution of various histone modifications. An important experimental goal is to compare the ChIP-seq profiles between an experimental sample and a reference sample, and to identify regions that show differential enrichment. However, comparative analysis of samples remains challenging for histone modifications with broad domains, such as heterochromatin-associated H3K27me3, as most ChIP-seq algorithms are designed to detect well defined peak-like features.

Results

To address this limitation we introduce histoneHMM, a powerful bivariate Hidden Markov Model for the differential analysis of histone modifications with broad genomic footprints. histoneHMM aggregates short-reads over larger region

SUBMITTER: Heinig M 

PROVIDER: S-EPMC4347972 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature