# Juicebox (Web)

We'll start with the lightweight version of Juicebox available on the web. Open a browser and type [`https://aidenlab.org/juicebox`](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!

{% hint style="success" %}
You can even browse 3D Genomics Hi-C maps on your mobile phone!
{% endhint %}

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

![](https://2157517455-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LijQZQE8sc7HbVdoxEA%2F-M7hw8UudYwDQh9qI6Dz%2F-M7i1B245RN7aDMEz3hz%2Fimage.png?alt=media\&token=3d215574-63e4-4d4b-8b69-01fa66c46d7f)

1. Click `Load Map → ENCODE`&#x20;
2. Choose the first map, the combined replicate  map `MboI primary+replicate GM12878`

![](https://2157517455-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LijQZQE8sc7HbVdoxEA%2F-M7hE2OFeI51tK-4lmbN%2F-M7hEjkko1_1hgLPMmlF%2Fimage.png?alt=media\&token=fccd403a-edd2-4961-8e77-5b3a4f8b7fbe)

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

![](https://2157517455-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LijQZQE8sc7HbVdoxEA%2F-M7DA47yODbP5k_EUxNw%2F-M7DFWdPi4AqiFrnBCXM%2Fgenome-wide.png?alt=media\&token=8bf514e6-e566-4384-abfe-f2680afc17af)

## 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

![](https://2157517455-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LijQZQE8sc7HbVdoxEA%2F-M7DA47yODbP5k_EUxNw%2F-M7DKC72TKOGfk9KRME6%2Fchromosomee.png?alt=media\&token=8aa0956a-9ff6-43d5-8873-37ffa66576f3)

This will load the chromosome-wide view.

![](https://2157517455-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LijQZQE8sc7HbVdoxEA%2F-M7DA47yODbP5k_EUxNw%2F-M7DGWtQ2k8733LqSBI_%2Fchr17.png?alt=media\&token=438d29b6-f81d-4645-aaac-e2f1c8237c77)

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

![](https://2157517455-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LijQZQE8sc7HbVdoxEA%2F-M7DA47yODbP5k_EUxNw%2F-M7DGqPLfgmh39soMAU_%2Fnorm_select.png?alt=media\&token=0a14e2d5-d512-41e7-8fc4-a28e176d6a03)

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.&#x20;

![](https://2157517455-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LijQZQE8sc7HbVdoxEA%2F-M7DA47yODbP5k_EUxNw%2F-M7DHPPo08jbrvLJ0I3S%2Fresolution.png?alt=media\&token=3c1416ad-ba6c-4e4a-bd62-4abf7637eb4d)

* 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.&#x20;

![](https://2157517455-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LijQZQE8sc7HbVdoxEA%2F-M7hE2OFeI51tK-4lmbN%2F-M7hGNM4W7PL-XKU5tX0%2Fimage.png?alt=media\&token=f18cd859-422d-4b0a-ac10-a9b54da2a6a2)

* 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.

![](https://2157517455-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LijQZQE8sc7HbVdoxEA%2F-M7DA47yODbP5k_EUxNw%2F-M7DK67eL9MRRLz3H7Wg%2Fdrag.png?alt=media\&token=17980170-0c6c-43f7-ae4e-bd7a19b419ef)

* 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:

![](https://2157517455-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LijQZQE8sc7HbVdoxEA%2F-M7DA47yODbP5k_EUxNw%2F-M7DKoJ8R90F9SKSW8Q2%2Fchr17_zoom.png?alt=media\&token=651feda4-1393-4a74-8b2d-b8e46a13c929)

