Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is an increasingly common experimental approach to generate genome-wide maps of histone modifications and to dissect the complexity of the epigenome. Here, we propose EpiCSeg: a novel algorithm that combines several histone modification maps for the segmentation and characterization of cell-type specific epigenomic landscapes. By using an accurate probabilistic model for the read counts, EpiCSeg provides a useful annotation for a considerably larger portion of the genome, shows a stronger association with validation data, and yields more consistent predictions across replicate experiments when compared to existing methods. The software is available at http://github.com/lamortenera/epicseg ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0708-z) contains supplementary material, which is available to authorized users.