Juicebox (Desktop)

Opening a .hic file

The first step is to download Juicebox from https://github.com/aidenlab/Juicebox/wiki/Download

Make sure you have Java installed on your system

Once you've successfully launched Juicebox, click File → Open... to load a new Hi-C map.

ENCODE Hi-C maps are listed under ENCODE Hi-C experiments. Click in-situ GM12878 MboI combined replicates (MAPQ 30) to open our largest map, the 6 billion read combined replicates GM12878 library.

The menu links to URLs that are automatically generated from the ENCODE API. As you can see from the dialog, you can also load a local map (useful if your internet connection is spotty) or load a map via a custom URL.

Juicebox can load Dropbox and Google Drive URLs – so you can upload a map to Dropbox for only your collaborators to access.

Once you've selected the Hi-C map, it will load and show all the chromosomes in a genome-wide view.

Zooming In

Click on chromosome 17. Using the selector on the left below Normalization, change the Normalization to Balanced. This is a way to compensate for various biases in the data.

There are several ways to zoom in:

• Slide the resolution slider to 5 KB. Use your mouse to pan until your range is roughly 64,500 KB to 69,000 KB.

• Go to 5 KB. In the Go panel, type 17:64500000-69000000 in both boxes and hit the refresh button. Go back to 5 KB if necessary.

• Look at the text on the right as you move your mouse on the heat map. Hold down the Alt key and draw a box that encompasses 64,500 kb to 69,000 kb.

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

If you ever get lost, you can double click in the mini map in the upper right; you can also move the box within that mini map. You can also right click within the map and select Jump to Diagonal