Fig. 4

Overlap, APA, and Peak plots (left to right) using primary GM12878 (chromosome 6 at 5 KB). FitHiC2 overlaps 95.3% across the analysis. Apart from that, HiCCUPS has the highest amount (45.9%) of overlap across three different datasets and FitHiChIP does not overlap any loops. SIP (30.6%), Mustache (19.1%), and Chromosight (25.4%) have a significant amount of overlap. cLoops and cLoops2 produce results only for primary and replicate data and the overlap percentage is around 1. FitHiC2 shows enrichment in different regions and has the strong enrichment compared with other tools. cLoops, cLoops2, and FitHiChIP have enrichment in the middle vertical region and they are almost in the same shape. HiCCUPS, SIP, Peakachu, and HiCExplorer have enrichment in the middle region. Peakachu, LASCA, and Chromosight have enrichment in the left lower corner from the center and Mustache shows enrichment in the center pixel. Though FitHiC2 creates a diagonal dark straight line marking peaks, Mustache and HiCExplorer mark the highest number of peaks. Chromosight, LASCA, and SIP mark peaks in the upper left and lower right corners near 20 M and 25 M region. HiCCUPS* and HiCExplorer** didn’t produce results at low resolutions and cLoops*** and cLoops2*** do not have a resolution parameter