Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping
Fig 5
Perm-seq analysis of GM12878 Ctcf and Sin3a ChIP-seq dataset with DNase-seq and Histone ChIP-seq priors.
(a) Heatmap of normalized DNase-seq and Histone ChIP-seq read counts for the [-1000 bps, +1000 bps] window anchored at GM12878 Ctcf peak summits depicted by the vertical dashed lines. Perm-seq-specific (DNase+Histone): Perm-seq optimal peaks using DNase-seq and Histone ChIP-seq in prior construction. These peaks are not identified when using only DNase-seq for prior construction or with CSEM. Perm-seq-specific (DNase): Perm-seq optimal peaks using only DNase-seq in prior construction. These peaks are not identified when using DNase-seq and Histone ChIP-seq for prior construction or with CSEM. (b) Heatmap of normalized DNase-seq and H2a.z ChIP-seq read counts for the [-500 bps, +500 bps] window anchored at GM12878 Sin3a peak summits. Perm-seq-specific (DNase): Perm-seq optimal peaks using DNase-seq in prior construction. These peaks are not identified when using only H2a.z ChIP-seq for prior construction or with CSEM. Perm-seq-specific (H2a.z): Perm-seq optimal peaks using only H2a.z ChIP-seq in prior construction. These peaks are not identified when using DNase-seq for prior construction or with CSEM. Next best mapping positions of Perm-seq-specific (DNase) peaks denote the regions where the multi-reads of the peaks map with the next best total allocation scores, i.e., ranked second compared to the allocation scores at the actual peaks.