Extended Data Fig. 2: Comparison of SnapHiC- and HiCCUPS-identified loops from mES cells.
From: SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data
a, Venn diagram of overlaps between SnapHiC- and HiCCUPS-identified loops (with default or optimal parameters) from 742 mES cells. b, c, Line plots showing the performance of SnapHiC and HiCCUPS applied to different number of mES cells (N=10, 25, 50, 75, 100, 200, 300, 400, 500, 600, 700 and 742). The dots represent the mean values of precision rate (b) and recall rate (c) across six randomly sampled subsets of mES cells from the 742 cells that passed our quality control (see details in Methods), respectively (except for N=742). The error bar represents the standard deviation calculated across six randomly sampled subsets. These values are also used to calculate the F1 score in Fig. 1c. If the lower bound of confidence interval (mean-sd) is less than 0, it is set as 0. For precision, recall and F1-score, if the upper bound of confidence interval (mean+sd) is greater 1, it is set as 1.
