Adding Track Hubs to Ensembl

Manually attaching a track hub

You have two ways to add a track hub to Region in Detail. First, if the track hub is public and registerd with Trackhub Registry then you can search the Trackhub registry itself. Second, you can manually add a track hub as follows:

  1. Click on the "Custom tracks" icon in the image toolbar or the lefthand button menu
  2. Fill in the data form:
    1. Give your track hub a name (optional - it will be parsed from the hub.txt file)
    2. The current species will be preselected - note that we now support multispecies hubs, so relevant data will be available on all appropriate species
    3. The assembly is automatically set to the current assembly for the species you are on - if you wish to use a track hub with data on older assemblies, you will need to use an archive site (not available for all Ensembl-powered websites, or for assemblies that predate our track hub code)
    4. In the large text box, type/paste the full URL of your hub's hub.txt file, e.g. http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/current_release/homo_sapiens/hub/hub.txt
    5. A dropdown box labeled 'Data format' will appear
      • If your hub file is called hub.txt, the form will automatically set the format to 'Track hub'
      • If it has a non-standard name, you will need to select 'Track hub' from the dropdown
    6. Click on the 'Add data' button
  3. When your hub has finished loading, a "Configure your hub" link will appear - click on it to see the configuration options for your tracks: [screenshot]

Programmatically attaching track hubs

If you wish to put a URL on your website which automatically attaches a hub to Ensembl, please use the following URL format:

http://www.ensembl.org/Trackhub?url=http://www.coolgenomics.ac.uk/hub.txt

For more precise configuration, you can add the following optional parameters, separated by semicolons:

  • Species - binomial name with underscores, as used by Ensembl URLs. E.g. Homo_sapiens
  • Location - coordinates as region:start-end, using parameter name 'r'

e.g. http://www.ensembl.org/Trackhub?url=http://www.coolgenomics.ac.uk/hub.txt;species=Homo_sapiens;r=X:123456-123789

Differences between Ensembl and UCSC

We aim to support as many features as we can from the track hub specifications, but in some cases there is no direct correspondence between the way UCSC displays its tracks and how Ensembl displays the same data. For example, a bigBed track can be configured as either 'full' or 'pack' in your trackhub, but both these UCSC display styles correspond most closely to Ensembl's 'structure with labels', so they will look identical in our genome browser.

Setting up a track hub

For how to set up a hub, see the documentation provided by UCSC, the originators of this data service: