Analysis - ChIP-Seq - Regional Enrichment

Introduction

This tool is used to identify statistically significant enrichment on regions that are defined relative to annotated regions of the genome, rather than to regions defined by the ChIP-Seq data itself.  It is typically used when the pattern of the ChIP-Seq target is so diffuse that standard peak callers have a difficult time identifying regions of enrichment.  In this case we will use regions that are of a priori interest, such as promoters, gene bodies, CpG islands , etc. that are likely regions to contain enrichment for the ChIP target.  The ngsc-chipseq-RegionalEnrichment tool counts reads on these pre-defined regions of interest for both a ChIP and a control (usually input) sample, then uses a Fisher exact test and Benjamini-Hochberg correction to assess the enrichment of the ChIP signal on the region.  A new track will be loaded with the enrichment ratio as the score and the p-value and FDR.

Details

A pseudocount of 1 is added to each region when computing the Fisher test.