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hic-pipeline

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End-to-end Hi-C analysis workflow from FASTQ to compartments, TADs, and loops, with the decision of WHICH features the sequencing depth can support. Covers pairtools read-pair processing and library QC, cooler matrices, ICE balancing and distance-decay expected, A/B compartments, TAD boundaries, loop calling, and the routing of HiChIP/PLAC-seq/Capture Hi-C to protein-directed loop callers. Use when processing Hi-C data end to end, deciding a resolution for a given depth, or choosing between bulk-Hi-C and protein-directed loop calling.

When to use

• processing Hi-C data end to end
• deciding a resolution for a given depth
• choosing between bulk-Hi-C and protein-directed loop calling
• pairtools read-pair processing and library QC
• cooler matrices
• ICE balancing and distance-decay expected
• A/B compartments
• TAD boundaries

When not to use

• de-novo loop calling on shallow maps
• generic dots/HiCCUPS for HiChIP, PLAC-seq, and Capture Hi-C

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