Juicebox (Web)

We'll start with the lightweight version of Juicebox available on the web. Open a browser and type https://aidenlab.org/juicebox or click the hyperlink.

Juicebox on the Web is run via client side JavaScript. Any hic file can be loaded from a URL – and in particular, .hic files uploaded to Dropbox, GEO, Google Drive, Amazon S3, or any web server can be streamed!

You can even browse 3D Genomics Hi-C maps on your mobile phone!

Juicebox on the Web makes it easy to browse maps side-by-side and to share exactly what you’re looking at with collaborators. The core functionality of browsing contact maps together with epigenetic marks is the same as Juicebox Desktop.

Loading Maps

  1. Click Load Map → ENCODE

  2. Choose the first map, the combined replicate map MboI primary+replicate GM12878

The genome-wide view will load for the .hic file.

Zooming In

Let's zoom in on chromosome 17. To select the chromosome from the genome-wide view, you can:

  • Click on the three bar "hamburger" icon in the right top corner, then select the chromosome under the dropdown menu

  • Click on the region of the Hi-C map corresponding to chromosome 17

  • Click on the numbered chromosome axis label

This will load the chromosome-wide view.

Let's change the Norm (Normalization) to Balanced. This balances the map to account for types of experimental bias in the data.

There are several ways to zoom in a Hi-C map. Let's zoom into the region around 69.4 MB to 72.3 MB. You can use one of the following methods:

  • Slide the resolution dropdown to 5 KB. Use your mouse to pan until your position is roughly 69.4 MB to 72.3 MB.

  • Type in 17:69,357,606-72,237,605 17:69,352,606-72,232,605 in the location text panel and press the enter key. Go to 5 KB if necessary.

  • Hold down the Alt key (Option key on Macs) and draw a box that encompasses 69.4 MB to 72.3 MB. Repeat as necessary and use the mouse to pan until you find the right location.

  • Zoom in further by clicking; the heat map will be centered at the point you click.

  • Use pinch zoom on a mobile device and pan as needed until you're at the target location.

  • Type in your gene of interest in the location text box to jump to the location.

You should see the following region: