Archive Ensembl HomeArchive Ensembl Home

Adding Custom Tracks to Ensembl

How to add custom tracks

Your custom tracks are managed using the pop-up control panel, accessed through the 'Manage your data' button under the left-hand menu.

You can add a track from any species-specific page, but it will only be displayed on suitable Location views, such as 'Region in Detail'.

Ways to add tracks to Ensembl

  1. Upload a file to our servers (max 5MB), from either your own computer or a location on the web (URL-based data).
  2. Attach a URL, from which the file will be read each time you visit a page that has the track on.
    • either by using the URL upload panel: Manage Your Data -> Attach Remote File
    • or by creating a specific URL for an Ensembl page that includes the location of your data file
  3. Attach a DAS (Distributed Annotation System) source, either from your own DAS server or anywhere else on the internet.
  4. Attach a BAM file using a url, which will be read each time you visit an Ensembl page with that track turned on. Note: both the BAM file and its index file should be present on your webserver. The BAM file should have a ".bam" extension, and the index file should have a ".bam.bai" extension. E.g. Mydata.bam and Mydata.bam.bai

Coordinate Systems

Use either chromosome or (finished) BAC clone coordinates in custom data sets.

Displaying Data on Whole Chromosomes

You can display uploaded and/or attached user data on the karyotype, or the chromosome diagram.

  1. Click on either Whole genome or Chromosome summary at the left of any Location page.
  2. Click the Configure this page button below the left-hand menu.
  3. Click on the User attached data link in the lefthand menu and select any tracks you would like to display.
  4. Click on the 'tick' button to Save and Close the window and view the data.

Note: for large data sets, your display options will automatically be limited to density plots rather than individual feature points.

Supported file formats

Click on a link for documentation on a format and its supported options.

Sample data files

Data access and security

Saving tracks

Uploaded data is saved temporarily to our filesystem and accessed via cookie, so you can only view it from the browser in which you uploaded it. For longer-term access to your data, you can save the track to our database server, but this requires an Ensembl user account. Once logged in, you will see a 'Save' link next to your track - click on this and the track will be transferred to the database and can be accessed on any computer where you are logged into Ensembl.

Remote data is not saved to the database. Only the URL or source name is saved to your user account, to allow you to access the file easily from any location, without having to reattach it.

Deleting tracks

The track will remain on your display while you navigate around the genome. To hide the track, choose the "no display" option (empty box) for that track in the Configure this page menu.

To remove the data set, click the Manage your data link at the left of Location. Click Manage data at the left of the window. The tracks you have currently uploaded and/or attached will be listed. Click delete next to any you wish to remove.

Data Upload Disclaimer

Although your data source is allocated a unique ID and any management operations on saved data (e. g. deleting) require a password, this is only trivial security. Data uploads are made on an open, non-secure network connection. If your data is sensitive you should not upload it but contact Ensembl for more information.

While we undertake everything to not make uploaded data available to any person other than the originator we DO NOT provide any assurance whatsoever concerning data security and/or privacy.

If you are concerned about data privacy you should consider setting up your own secure DAS server.