Fig. 3

A comparison between Mustache, SIP, and HiCCUPS reported loop calls in a region of chromosome 1 for the GM12878 cell line (50.75–51.75 Mb). The Hi-C contact map is rotated 45^∘ such that the main diagonal is horizontal (top). Below the contact map, we report genomic coordinates, gene annotations (genes on the negative strand are shown in red color), CTCF motifs and their orientation, and ChIP-seq signals for SMC3, CTCF, RAD21, H3K4me3, and H3K27ac (coverage tracks plotted by HiGlass). The bottom row demonstrates loop calls as arcs connecting two loci labeled by the initial letter of the methods by which they are detected (“M” for Mustache, “S” for SIP, and “H” for HiCCUPS)