Additional Resources

There are many other features to explore in Juicebox Desktop! Right click in the heat map to see some of them. Within the File menu, you can look at Dataset Metrics or export the current data shown on the screen. The View menu gives some options for looking at the data, including the Submapping function, changing the heat map color, exporting the map for a figure, and more. Within the Annotations dialog, you can load your own 1D and 2D annotations. The Bookmarks menu allows you to save a location to quickly go back to it between sessions. The Assembly menu is for using Juicebox for Assembly Tools to correct genome assemblies.

Post any questions to our forum! https://aidenlab.org/forum.html

Aiden Lab - The Center for Genome Architecture - Baylor College of Medicine

Juicebox (Desktop) code and documentation: https://github.com/aidenlab/juicebox/wiki

Home · aidenlab/Juicebox WikiGitHub

Juicebox (Web) code and documentation: https://igvteam.github.io/juicebox.js

juicebox.jsjuicebox.js

Embedding your own Juicebox: https://igvteam.github.io/juicebox.js/docs/embedding

juicebox.jsjuicebox.js

Papers
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326 (2009).
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014 Dec 18;159(7):1665-80.
Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Systems. 2016 Jul 27;3(1):99-101.
Juicebox.js provides a cloud-based visualization system for Hi-C data. Cell Systems. 2018 Feb 28;6(2):256-8.
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science. 2017 Apr 7;356(6333):92-5.
The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv. 2018 Jan 1:254797.