Fig. 5

Impact of scHi-C normalization and de-noising methods on the compartment and domain detection for GM12878. Comparison of detected topologically associating domains (TADs) and A/B compartments between bulk GM12878 Hi-C data on chromosome 1 (upper right triangles) and the aggregated single-cell Hi-C data (lower left triangles) after normalization or de-noising using Kim2020 data set. The numbers after the red squares at the left bottom or right upper corner of each contact matrix represent the minimum interaction frequency for the reddest locus pair. The black arrow highlights one example region that keeps showing over-imputation artifacts by Higashi across all five cell types compared to the bulk Hi-C data as a gold standard. True cell labels for GM12878 were utilized to aggregate the processed scHi-C data. First row: The insulation scores [36] that trace the TAD boundaries are depicted on the contact matrices with gray lines corresponding to bulk Hi-C data and purple for BandNorm, blue for scVI-3D, green for Higashi, and yellow for scHiCluster. Second row: A/B compartments are detected using the eigenvector of the correlation map of bulk (upper right triangles) or aggregated (lower left triangles) Hi-C matrices, values of which are displayed above each correlation matrix