Fig. 6

Four example regions showing Mustache, HiCCUPS, and SIP reported loops. Mustache, HiCCUPS, and SIP loops are represented by blue circles, red filled circles, and green squares on the lower diagonal matrices, respectively. The upper diagonal matrices were left untouched in order to allow visualization of contact patterns in the underlying Hi-C data. The loop calls of the three methods using GM12878 Hi-C data are shown for a 50.75–51.75 Mb region of chromosome 1, b 12.5–13.4 Mb region of chromosome 12, c 88.7–88.5 Mb region of chromosome 4, and d 67.2–68Mb region of chromosome 1