Additional file 1 of UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity

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Additional file 1: PDF document containing all supplementary figures. Fig. S1. UnionLoops corrects false dataset specificity of chromatin loops in the conventional method, as demonstrated by biological replicate comparisons. Fig. S2. Schematic plot illustrating UnionLoops’ additional filtering of singletons whose anchors do not overlap with boundaries of any non-singleton clusters after pooling enriched pixels from all samples. Fig. S3. Percentage of loops rescued exclusively by MEGA among all rescued loops at each time point. Fig. S4. In contrast to centroids, a substantial number of singletons in each sample remained unclustered and lacked adjacent enriched pixels after pooling across all samples. Fig. S5. UnionLoops improves sensitivity and positional precision of HiCCUPS loop calls at five time points. Fig. S6. UnionLoops improves loop specificity across hESC, DE, PGT, PP, and SC-β organoids compared to the conventional method. Fig. S7. Quantification of loop strength based on local enrichment. Fig. S8. The differences in two operational features allow UnionLoops to uniquely rescue filtered loops and achieve better positional precision than Mariner. Fig. S9. UnionLoops improves loop precision for SIP and Mustache loop callers. Fig. S10. UnionLoops improves loop specificity for both SIP and Mustache loop callers compared to the conventional method. Fig. S11. Loop strength trajectories of loops shared across all samples.

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