DANIO-CODE is out – how can you work with it in Ensembl?

Functional genomics data from DANIO-CODE has been released to the public. This international effort, similar to ENCODE in human and mouse, seeks to characterise the functional elements in the zebrafish (Danio rerio) genome. Announced on Saturday at the International Zebrafish Conference, the DANIO-CODE dataset exists as a track hub, which can be viewed in Ensembl.

DANIO-CODE aims to include data from ChIP-seq, CAGE-seq, RNA-seq, ATAC-seq, Ribo-seq and meDIP-seq experiments on different zebrafish tissues and developmental stages, to functionally annotate genomic regions. The latest data-freeze (Freeze 2) has RNA-seq, histone modifications and transcription factor binding data available.

The track hub released by DANIO-CODE is easy to view in Ensembl. However, since the data was aligned to the GRCz10 genome, you’ll need to use the release 91 archive site (or older) to view it. Go to the zebrafish homepage, then click on the link, “Display your data in Ensembl”.

The zebrafish homepage in Ensembl 91


This will open a pop-up where you can paste in the URL of the hub https://danio-code.zfin.org/trackhub/DANIO-CODE.hub.txt. You’ll need to select “Track Hub” from the format selector.

The menu for adding custom tracks, including track hubs


Once you’ve attached the hub, you can configure which tracks to see in the normal Configure this Page menu on the region view.

The DANIO-CODE track hub in the Ensembl configure menu


You can choose which tracks you want to see, then close the menu to see the the data against the Ensembl features such as genes and variants.

An Ensembl region with some DANIO-CODE tracks added from the track hub

If you’re working with the DANIO-CODE track-hub and have any technical queries about the hub itself, you can contact the DANIO-CODE DCC technical helpdesk, or if you have any questions about data re-use and publication, try their general helpdesk.