Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data
Figure 3
BCP was robust, providing consistent results in replicate and at various coverage depths.
Using a second H3K36me3 data set and sub-samplings of the full replicate one dataset (30–90% randomly selected reads), we evaluated the reproducibility of BCP island calls. A) Enriched regions coinciding with gene coordinates were captured by the large, contiguous BCP islands (blue), while SICER islands (red) were more fractionated. B) We quantified the reproducible fraction of the full data set results versus the sub-samples (the number of full dataset island bases covered by a replicate/sub-sample island divided by total bases in full dataset islands, averaged across all islands) and vice versa. Also, we computed the fraction of island basepairs overlapping genic and intergenic regions (number of islands bases covered by genic/intergenic annotation divided by total bases in island, average across all islands).