hic-aggregationlisted

# Aggregate Hi-C Chromatin Contacts Across Studies ## When to Use - User wants to build a comprehensive catalog of chromatin loops from multiple Hi-C experiments - User asks "what regions are in 3D contact in my tissue?" or "aggregate loop calls across donors" - User needs a union catalog of BEDPE loops with resolution-aware anchor matching - User wants to identify high-confidence loops supported by multiple experiments - Example queries: "aggregate Hi-C loops for K562", "combine chromatin contacts across labs", "find consensus TAD boundaries in liver" Build a comprehensive catalog of chromatin loops for a tissue/cell type by merging BEDPE loop calls from multiple ENCODE Hi-C experiments. ## Scientific Rationale **The question**: "What regions are in 3D physical contact in my tissue?" Like histone marks and accessibility, chromatin loops are a **detection question**. If a loop between Region A and Region B is detected in one donor but not another, the contact is still real — individual variation, sequencing depth, and computational resolution explain absence. We want the **union of all detected contacts**. ### Key Concepts **Hi-C data** measures pairwise chromatin interactions genome-wide. After processing: - **Contact matrix** (`.hic` file): Genome-wide interaction frequencies at multiple resolutions - **Loop calls** (BEDPE): Statistically significant point interactions (loops) identified by algorithms like HICCUPS or Juicer - **TAD boundaries**: Topologically associ