Begin by loading a contact map (hic) file using
Load Contact Map > Select Contact Map. The menu list is searchable.
The viewer will initially open on the first chromosome in the file on both axes of the map display.
Navigate to locus
1:35,294,888-79,647,754 1:34,982,544-79,335,410. Entering only one locus will display the same locus on both map axes.
Pan and zoom
2D Annotations. A panel will pop up that will all you to change track colors, rearrange the track order, and remove tracks.
In addition to the provided menus, .hic contact map files and track files can also be loaded from the local file system or by URL. All common genomic track file formats are supported (bigwig, begbed, wig bedgraph, bed, gff3, and gtf). The supported 2D annotation format is described in the desktop Juicebox documentation.
View and compare two or more maps. Click on the
+ button above the map panel to create a new empty panel, and load another contact map. Note that all maps must be based on the same genome assembly.
For users of hosted instances at [aidenlab.org](https://aidenlab.org/juicebox] or igv.org the visualization state can be captured and shared by using the
Share button. The generated URLs encapsulate the current state of the application with the exception of locally loaded files (that is, files loaded from the user’s local file system). Files shared via juicebox URLs can be public or private, and can be shared with anyone who has access to the files. The URLs do not have an expiration date.