Hi-C track

Hi-C captures genome-wide chromatin interaction frequencies by sequencing pairs of genomic regions that are physically co-located in the nucleus. JBrowse renders these as a triangular contact matrix where color intensity indicates contact frequency — brighter means more interactions.

JBrowse reads .hic files produced by Juicer, Juicebox, and compatible pipelines, using the hic-straw module.

Loading a Hi-C track

In the Add track dialog, paste the URL to a .hic file (or open it from disk). JBrowse auto-detects the format and creates a Hi-C track. The track renders a triangular contact matrix below the chromosome ruler.

Reading the contact matrix

Hi-C contact matrix for a region of hg19 (~chr19:50–60 Mb). The diagonal (brightest red strip) represents self-interactions. Triangular blocks of elevated signal along the diagonal are topologically associating domains (TADs) — genomic regions whose loci contact each other more than they contact flanking regions. Off-diagonal bright spots are chromatin loops connecting specific pairs of loci.
Hi-C contact matrix for a region of hg19 (~chr19:50–60 Mb). The diagonal (brightest red strip) represents self-interactions. Triangular blocks of elevated signal along the diagonal are topologically associating domains (TADs) — genomic regions whose loci contact each other more than they contact flanking regions. Off-diagonal bright spots are chromatin loops connecting specific pairs of loci.

Key features to interpret:

  • Diagonal — always the brightest band; self-interactions within a region
  • TAD boundaries — sharp drops in signal that delimit the triangular blocks; the corners of these blocks are where loop anchors often occur
  • Loops — punctate off-diagonal bright spots at specific locus pairs, typically CTCF-anchored
  • Compartments — at low resolution, alternating plaid-like patterns (A/B compartments) reflecting active vs repressed chromatin

Adjusting resolution and color scale

JBrowse automatically selects a resolution that fits the current view width. Zoom in to increase resolution; zoom out to see larger-scale organization.

The color scale is configurable via the track's configuration — see the Hi-C track config guide for available options.

Live demo — Hi-C contact matrix with gene annotations