Fig. 1

Schematic HiCdat workflow. (a-b) After sequencing and initial quality checks have been performed, the read-ends (f: forward, r: reverse) are aligned separately to a reference genome. (c-d) After pairing the separately aligned read-ends, each end is mapped to genomic fragments, which are either genomic bins with a fixed size or restriction fragments with variable size. (e) Genomic fragments can be associated with various data types to test for correlation and enrichment of Hi-C data with genomic and epigenomic features. (f) Finally, the data can be conveniently analyzed in R using HiCdatR