Cooltools: Enabling high-resolution Hi-C analysis in Python
Fig 2
Expected and contact frequency versus distance.
a. Observed contact map for HFF Micro-C for chr2 and chr17 at 1Mb. Chromosomal arms p and q are depicted as light and dark grey rectangles respectively. Note the wide unmappable centromeric regions (white rows and columns) between chromosomal arms. Accounting for these regions is a key aspect of calculating an expected map. b. Expected map for three classes of regions: intra-chromosomal intra-arm, intra-chromosomal inter-arm, and inter-chromosomal. Regions for expected are specified using genomic views, where individual regions are chromosomal arms. Note that intra-chromosomal expected has a strongly decreasing contact frequency with genomic distance, whereas inter-chromosomal expected appears flat. c. Average contact frequency versus genomic separation, or P(s), for intra-arm interactions (blue, orange) and for inter-arm interactions (green), calculated from contact maps at 10kb. P(s) curves are matched by region and color with arrows on the middle heatmap.