Zerone: a ChIP-seq discretizer for multiple replicates with built-in quality control.

ABSTRACT:

Motivation

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the standard method to investigate chromatin protein composition. As the number of community-available ChIP-seq profiles increases, it becomes more common to use data from different sources, which makes joint analysis challenging. Issues such as lack of reproducibility, heterogeneous quality and conflicts between replicates become evident when comparing datasets, especially when they are produced by different laboratories.

Results

Here, we present Zerone, a ChIP-seq discretizer with built-in quality control. Zerone is powered by a Hidden Markov Model with zero-inflated negative multinomial emissions, which allows it to merge several replicates into a single discretized profile. To i

SUBMITTER: Cusco P 

PROVIDER: S-EPMC5039920 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature