Public Track Hubs

Ensembl Genomes provides support for track hubs as a way of sharing large quantities of annotation over the internet. A searchable list of public track hubs is available from the Track Hub Registry.

You can search the list of public track hubs from the Track Hub Registry itself, in which case you can use a direct link to allow you to attach the track hub to Ensembl or UCSC. Alternatively, to search for track hubs from within Ensembl, go to Region in Detail, click 'Add your data' and select 'Track Hub Registry Search' from the lefthand menu.

→ See the Track Hub Registry search for Arabidopsis thaliana.

If you wish to use a track hub that is not in the Trackhub Registry, please see our instructions on how to attach a track hub.

Please note that the tracks turned on by default are defined by the track hub provider. If there are a large number of these then the hub may be slow to load, or (in extreme cases) unable to load. After loading a hub, users are offered a link to a menu where they can configure which tracks shoild be turned on before they attempt to visualise any data, and use of this link is strongly advised.

Track hubs for all public RNA-Seq studies in plants

As part of a BBSRC funded crop infrastructure project, we have established a pipeline for generating track hubs for all public RNA-Seq studies in the INSDC archives. The pipeline discovers and aligns reads from RNA-Seq studies across all plant species in Ensembl Plants. Alignments and their associated metadata are registered in the Track Hub Registry for search and discovery within the genome browser.

In detail, the pipeline uses the ENA's search APIs to discover all plant spcific RNA-Seq studies. The read data for each study is aligned to the appropriate reference genome in Ensembl Plants using the iRAP pipeline developed by the EMBL-EBI Gene Expression team. Quality-filtered reads are aligned using TopHat 2. The resulting BAM files are converted to CRAM format. Each set of CRAM files for a specific study, along with their assocaited sample and study metadata are used to create a track hub that that registered in the Track Hub Registry.