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HiGlass is a tool for exploring genomic contact matrices and tracks. Please take a look at the examples and documentation for a description of the ways that it can be configured to explore and compare contact matrices. To load private data, HiGlass can be run locally within a Docker container. The HiC data in the examples below is from Rao et al. (2014) [2].

The paper describing HiGlass is published in Genome Biology [1].

Single View

Two Linked Views

HiGlass can also be configured to show two or more views. These views can be synchronized to always show the same location. For more information, please see the documentation about replacing tracks, adding new views, and synchronizing the locations of different views.

Classic Genome Browser Layout

If the 2D view is omitted, HiGlass functions like a regular 1D genome browser. See the documentation for more information about the different available track types and how to add them. Blue gene annotations are on the + strand while red annotations are on the - strand. This view shows a gene annotations track as well as four ENCODE data tracks containing ChIP seq profiles (H3K27ac, H3K4me1, H3K4me and H3K27me3).

Genome Browser Layout With Detail Views

All of the inter-view operations, such as linking and viewport projection are also available in the simplified genome browser layout. The example below shows a zoomed-out overview on top as well as two detail views below. The positions of the detail views are shown on the overview using viewport projections. Blue gene annotations are on the + strand while red annotations are on the - strand. The data is from Busslinger et al (2017) [3] and shows the accumulation of cohesin at sites of convergent transcription in CTCF / Wapl double knock-out mouse embryonic fibroblasts.


[1] Kerpedjiev, Peter, et al. "HiGlass: Web-based visual comparison and exploration of genome interaction maps." Genome Biology (2018): 19(125).

[2] Rao, Suhas SP, et al. "A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping." Cell 159.7 (2014): 1665-1680.

[3] Busslinger, Georg A., et al. "Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl." Nature 544.7651 (2017): 503-507.