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Adding Custom Tracks to gEVAL

How to add custom tracks

You can add a track from any species-specific page, such as Region in Detail. The track will automatically display in the view in which you have added it. You can also display an uploaded track in other views like Region Overview and the whole Chromosome. To do so, click the Configure this page button at the left, and select the track within the Your data menu.

To attach or upload a custom track, click the Add your data button at the left of most Ensembl views (which reads Manage your data if you already have added custom data) and upload or attach a file (see more about file types further in this document) in the resulting window. Alternatively, if you have clicked on Configure this page, add data by navigating to the Custom data tab in the configuration window and click on Add a custom track.

To upload and display data on a Karyotype view, click the Add your data or Manage your data button at the left. At the left of the resulting menu, click Features on Karyotype. Add IDs (such as Gene IDs like ENSG00000012048, ENSG00000139618, ENSG00000198668) or names (such as Gene names like BRCA1, BRCA2, CALM) into the box. Click the Show features button to view them along the karyotype.

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

Ways to add tracks to gEVAL

  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 Add your data link (or Manage your data if you already have custom data in gEVAL)
    • or by creating a specific URL for a gEVAL page that includes the location of your data file

Coordinate Systems

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

Trackhubs

Trackhubs also known as datahubs are web-accessible directories of genomic data that can be attached to genome browsers. The trackhub specifications were designed by the UCSC genome browser team and intended for use with that browser. For more information about trackhubs please visit this site.

Currently trackhubs consisting of composite tracks of subgroups, vcf and bam are not supported, but will be in the future.

NOTE: Remote hubs may be slow to load or unavailable.

Examples (more public trackhubs can be found here)

Trackhub nameDescriptionSpecies and assembly
GRC TrackhubGRC curated issues, sequence anomolies, component join certificates, lightweight optical/genome map info
  • Human - GRCh37, GRCh38
  • Mouse - NCBIm38, GRCm38
  • Zebrafish - Zv9, GRCz10
Porcine DNA methylation and gene transriptionDNA methylation and gene expression levels for eight tissues from the adult female Duroc chosen for production of the swine reference genome (TJ Tabasco)
  • Pig - Sscrofa10.2

Supported file formats

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

Sample data files

Data access and security

Saving and sharing 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 (unless you click the share icon as below).

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.

If you display your data on a Location view such as Region in Detail, click the sharing icon, or the Share this page button at the left, to send the same view, including your own track, to a labmate or collaborator.

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 gEVAL 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.