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The extremely large number of possible pairwise interactions in Hi-C samples imposes limitations on the realistically achievable sequencing depth at individual interactions, leading to reduced sensitivity. The recently developed Capture Hi-C (CHi-C) technology uses sequence capture to enrich Hi-C material for multiple genomic regions of interest (hereafter referred to as “baits”), making it possible to profile the global interaction profiles of many thousands of regions globally (“many vs all”) and at a high resolution.
(Cairns et al., 2016) CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data. Genome Biol.