HIGHLIGHTS
SUMMARY
The authors compare RefHiC against tools that do not use reference samples and find that RefHiC outperforms other programs at both topological associating domain and loop annotation across different cell types, species, and sequencing depths. To obtain a loop or TAD boundary score for bin pair (i, j) (with i ≠ j for loops and i=j for TAD boundaries), an encoder projects the submatrices centered at (i, j) in both the study sample and reference panel to low-dimensional embeddings. Most TFs are more strongly enriched at RefHiC loop predictions than at Chromosight loop . . .
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