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Adding Track Hubs to Ensembl

Manually attaching a track hub

If the track hub you are interested in is not in the Track Hub Registry, you can manually add it by filling in the 'Custom Tracks' 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
  7. On the next page, click on the "Configure your hub" link to see the configuration options for your track.

Configuring multidimensional track hubs

Some track hubs, such as the Blueprint Hub, are multidimensional. There is a specific interface to configure them. For the Blueprint Hub, you have two options: You can configure the ‘Blueprint Region’ or ‘Blueprint Signal’ display.

  1. Select your tracks from a matrix based on the two primary dimensions, as decided by the Track Hub provider. For Blueprint these are the sample description (here a cell type) and experiment (here a data type) you are interested in. You can do this by selecting or deselecting all and by selecting individual sample descriptions or experiments. You can use the search box at the top of each tab to help you find the data you are interested in. Now click on the green ‘Filter tracks’ button at the bottom.
  2. Refine your selection based on other dimensions to the data, for example analysis_group or analysis_type (note this screen is not shown for Track Hubs with two dimensions only). Click on the cells in the matrix to select what you want to see. Now click on the green ‘Configure track display’ button at the bottom.
  3. Configure your track display. Click on the cells in a similar matrix to select what you want to see.
  4. Click on the green ‘View tracks’ button at the top to load and display the data you have selected and you are done. [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

Important note: You must use semicolons, not ampersands, between parameters, otherwise your track hub will not attach. This is because some track hubs use dynamic URLs containing question marks and ampersands, which need to be encoded separately from the other parameters passed to the Ensembl URL.

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: