Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping
Fig 1
Discriminative power of DNase-seq for mapping locations of multi-reads.
(a) Log base two ratios of DNase-seq versus ChIP-seq read counts in the local neighbourhoods of the two mapping locations of each multi-read in Gata2 ChIP-seq dataset (Huvec). The vertical and horizontal lines depict boundaries with the log base two ratios equal to 0.5. The proportion of read pairs in categories: ChIP: ChIP or both ChIP and DNase discriminates; Neither: Neither ChIP nor DNase discriminates; Only DNase: Only DNase discriminates; Opposite: ChIP and DNase log base 2 ratios have different signs are 23%, 44%, 26%, and 7%, respectively. (b) Classification of multi-reads with two mapping locations based on their local DNase-seq and ChIP-seq read counts into 4 groups as ChIP, Neither, Only DNase, and Opposite. (c) Overall summary of the Perm-seq pipeline.