> For the complete documentation index, see [llms.txt](https://aidenlab.gitbook.io/juicebox/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://aidenlab.gitbook.io/juicebox/desktop.md).

# Juicebox (Desktop)

## Opening a *.hic* file

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

{% hint style="info" %}
Make sure you have Java installed on your system
{% endhint %}

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

![](https://2157517455-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LijQZQE8sc7HbVdoxEA%2F-Lj2gavu4NTsjkOUMYaT%2F-Lj2iPzuTl6_GJ2UaMRK%2FScreen%20Shot%202019-07-05%20at%202.59.08%20PM.png?alt=media\&token=cbad2dfe-167f-4c85-b636-bc69bd42ad4e)

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.

![](https://2157517455-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LijQZQE8sc7HbVdoxEA%2F-Lj2gavu4NTsjkOUMYaT%2F-Lj2itcLY6fG3-XBhzND%2FScreen%20Shot%202019-07-05%20at%203.02.45%20PM.png?alt=media\&token=ee3c9498-eab5-408e-8dce-59347f6a6e21)

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.

{% hint style="success" %}
Juicebox can load Dropbox and Google Drive URLs – so you can upload a map to Dropbox for only your collaborators to access.
{% endhint %}

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

![](https://2157517455-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LijQZQE8sc7HbVdoxEA%2F-Lj2gavu4NTsjkOUMYaT%2F-Lj2js_V0JRQoDXKpVvE%2FScreen%20Shot%202019-07-05%20at%2012.51.13%20PM.png?alt=media\&token=fdae559d-237e-45dd-a0dd-a12a22ff7506)

## 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.&#x20;
* 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.&#x20;
* 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.&#x20;
* Zoom in further by clicking; the heat map will be centered at the point you click.

{% hint style="info" %}
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`
{% endhint %}

![](https://2157517455-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LijQZQE8sc7HbVdoxEA%2F-LjHGrNQoU2s2fZsKryI%2F-LjHIqkHxra_j5GkpWwC%2FScreen%20Shot%202019-07-05%20at%2012.51.26%20PM.png?alt=media\&token=7eee57a2-2c4d-45df-9a62-f8fd7facae1d)