Fig. 3

Evaluating the reliability of loop anchors. A UV Rate of ChIA-PET analytical methods across all ChIA-PET datasets. B UV rate of HiChIP analytical methods across all HiChIP datasets. C Comparison of UV Rate between ChIA-PET and HiChIP datasets. D Number of loops identified with different computational methods across all datasets. Bar graph displays the distribution of PET counts. The red line represents the average PET counts for the corresponding loop sets. E The peak co-occupancy (PC) of peak-based loop anchors. F Pearson’s correlation between PC and anchor length. G Pearson’s correlation between PC and peak size. R, correlation coefficient. p value calculated by t-test. H Global ES of two cluster-based methods in all datasets. *** p value < 1e−3, p value was calculated by t-test. I The overlap between mESC-Smc1 ChIP-seq peaks, peak-based anchors, and cluster-based anchors. J The genomic annotation of mESC-Smc1 ChIP-seq peaks, peak-based anchors, overlapping anchors, and cluster-specific anchors. All the error bars represent the calculated mean and standard error