Figure 2. Overview of experimental artefacts generated by the Hi-C experimental protocol.

The schematic shows the genome digested into 5 restriction fragments. These fragments may subsequently ligate to each other, or fragments derived from another chromosome, forming valid cis or trans di-tags respectively ( a). In contrast, re-ligation or incomplete digestion leads to the generation of invalid contiguous sequences ( b). Another common artefact occurs when the sequenced read-pair maps to a single restriction fragment ( c), ( d) & ( e). Further, PCR may result in a fragment being copied multiple times ( f). Di-tags are also rejected when the mapped reads are positioned too far away from the putative restriction enzyme cut-site than allowed by the experimental size-selection step ( g).