Loading Annotations (Annotations menu)
Make sure you have a Hi-C map open. From the Annotations menu, click Load Basic Annotations...
A pop up window titled *Available Features* will appear.
Check the required feature(s) and press "OK". The new annotation will be downloaded to your Juicebox viewer and displayed above and to the left of the main map window. Note that some annotations, like the gene track, are clickable, showing more information.
In order to remove the annotation, right click on the track, and select "Remove track", or you can also repeat the steps above and uncheck the annotation(s) you want to remove.
Additional annotations include:
Gene reference:
Coverage annotation:
GM12878 CTCF orientation annotation:
Eigenvector:
You can also load you your own bed or wig track files. From the Annotations menu, click Load Basic Annotations...
Click Add 1D.... A file explorer window will open. Select your track file. The new track file name will appear in Available Features menu. Click "OK" to show your track. In case of an unsupported file format, the following error will be displayed:
Some of the annotations in Juicebox are marked on the main map. An example is available in the GM2878 in situ MBOI primary + replicate map. After opening this map, a "Data-set specific 2D features" annotations are available in the annotations menu. Use the F2 key to toggle the visibility of 2D annotations.
Juicebox supports the bedpe format for 2D annotations and uses this format for writing loop and domain files. Bedpe files are tab-delimited. The header line looks like this:
#chr1 x1 x2 chr2 y1 y2 name score strand1 strand2 color [optional fields]
chr5 85000000 89000000 chr5 85000000 89000000 . . . . 255,0,0
For backwards compatibility, we still support the below format as well, but encourage everyone to use bedpe instead.
chr1 x1 x2 chr2 y1 y2 color comment
chrX 85000000 89000000 chrX 85000000 89000000 0,255,0 My green region
chrX 90000000 99100000 chrX 90000000 99100000 0,0,255 My blue region
Save the example as a text file. Load it into Juicebox by going to Annoations>Load Basic Annotations...>Add 2D.... You should see the following result:
Note:
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Make sure your chromosome names are the same as the ones that appear in the Hi-C map.
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Keep the header line.
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The file is tab delimited.
You can also create custom data-specific 2D annotations to visualize peaks and domains. In order to create a custom annotation, open a Juicebox map (GM2878 in situ MBOI primary + replicate, for example) and hold the shift key over a region of the map. A moving cross-hairs will appear as you move the mouse.
In order to create a custom 2D annotation for a particular region of interest, hover the mouse over a region of the map that is enriched higher compared to the surrounding area. By clicking on this region, a small box will appear on both sides of the diagonal line indicating the successful annotation.
To create a custom annotation for a broader region, hold the shift key and use the mouse to again create the moving cross hairs. Click and drag the mouse to highlight a square around the area that is to be annotated. A green rectangle will appear and border the region of interest. If you annotate close to the diagonal, the annotation will auto-capture the region as a square.
You can also use Juicebox to display ENCODE tracks. From the Annotations menu, click Load Basic Annotations...
Click Load ENCODE Tracks. The Encode Production Data screen will appear:
You can use free text to search through any of the track fields, or scroll through the tracks list. Check the required ENCODE track(s) and click "Load" to load the data. A track will be added to top and left of the main map.
With some tracks, you can change basic appearance. Right click on a track and select Configure track....
A new screen will appear, where you can change track Name, Min/Max values Scale, and colors for positive and negative values.
Annotations can be edited within Juicebox. Users can adjust an annotation's position, delete it, change its color, or add a text attribute to document any interesting features. Hand annotations can be edited directly, following the directions below. Loaded 2D annotations can also be edited by copying them to hand annotations. To do this, load a basic 2D annotation, then go to Annotations → 2D Annotations → Copy to Hand Annotations. The loaded annotation can now be edited as a hand annotation.
To adjust the size of the annotation, hover over the upper lefthand or lower righthand corner, inside of the annotation.
Click and drag the corner to the desired size. Release the mouse to create the change.
Attributes can be added to annotations to mark interesting features. For example, an attribute name could be "Feature Quality", and its value could be "Poor,""High," etc. To add an attribute, right click an annotation and go to Configure Feature → Change Attributes. An attribute can be added by entering a name, or descriptive category, and value. The attribute will be displayed as a part of the hover text on the righthand bar of the main window.
To edit an attribute, right click an annotation, go to Configure Feature → Change Attributes. The value of the attribute can now be changed, as shown below.
The color of an annotation can be changed by right clicking an annotation and going to Configure Feature → Change Color.
Individual annotations can be deleted by right clicking an annotation and going to Configure Feature → Delete. The last added annotation can also be removed by going to Annotations → Hand Annotations → Undo Annotation, or by pressing "Z", the shortcut key.
A set of hand annotations can be exported by going to Annotations → Hand Annotations → Export...
Exported annotations can be loaded as a basic 2D annotation, by selecting the file by going to Annotations → Load Basic Annotations... → Add 2D...
Let's see some more features for exploring the map.