GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis

Georg Stricker, Alexander Engelhardt, Daniel Schulz, Matthias Schmid, Achim Tresch, Julien Gagneur

Abstract: Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is a widely used approach to study protein–DNA interactions. Often, the quantities of interest are the differential occupancies relative to controls, between genetic backgrounds, treatments, or combinations thereof. Current methods for differential occupancy of ChIP-Seq data rely however on binning or sliding window techniques, for which the choice of the window and bin sizes are subjective.