Fig. 2

FAN-C matrix generation. a-c Schematic overview of the matrix generation pipeline. a Mapping features. b Processing and filtering of Hi-C read pairs. c Assembly, filtering and normalisation of the Hi-C matrix from valid read pairs. d–f FAN-C statistics plots using data from HUVEC Hi-C [25]. d Ligation error plot as in [52, 53]. Dashed line indicates expected values. e Density plot of the sum of restriction site distances (insert size) measured from the mapping location of a read to the nearest restriction site. Dashed line indicates median insert size. f Summary statistics plot showing the read pairs removed by various filters. g Coverage plot of a Hi-C matrix binned at 1 kb resolution. Dashed line indicates the chosen coverage cutoff at 25% median coverage