Fig. 1: Pore-C experimental and data workflow.

a The Pore-C experimental protocol, which captures pairwise and multi-way contacts (see Methods). b Representation of multi-way contacts at different resolutions (top). Incidence matrix visualizations of a representative example from Chromosome 8 in adult human fibroblasts at each resolution (bottom). The numbers in the left columns represent the location of each genomic locus present in a multi-way contact, where values are either the chromosome base-pair position (read-level) or the bin into which the locus was placed (binning at 100 kb, 1 Mb, or 25 Mb). c Hypergraph representation of Pore-C contacts (left) and an incidence matrix (right) of four multi-way contacts within (yellow-to-yellow) and between (yellow-to-purple) chromosomes. Contacts correspond to examples from (a). The numbers in the left column represent genomic bins in which a locus resides. Each vertical line represents a multi-way contact, with nodes at participating genomic loci. d Multi-way contacts can be decomposed into pairwise contacts. Decomposed multi-way contacts can be represented using graphs (left) or incidence matrices (middle), which when decomposed are interchangeable with traditional Hi-C contact matrices (right). Contacts correspond to examples from (a) and (c). e Flowchart overview of the computational framework. Descriptions of file type formats (red text) are in Supplementary Table 1.