Aggregate Hi-C chromatin contact maps across studies

Aggregate and normalize Hi-C contact matrices across samples

Comparing 3D genome structure across cell types by aggregating replicate Hi-C experiments

• · .hic files
• · resolution (e.g. 5kb, 10kb)

• · aggregated contact matrix
• · normalized compartment calls

• · Juicer tools
• · HiCRep or Cooltools

Input .hic files in standard format (Juicer)

• · Normalization artifacts at low coverage
• · Resolution mismatch between samples
• · Batch effects not corrected

• · Juicer/Cooltools documented standards