PAG 2019 Workshop: Exploring your data in Ensembl (Digital tools and resources)

Date:

  Monday 14 January 2019

Venue: 

Town and Country Hotel - 500 Hotel Circle North,  San Diego, , CA,  92108,  United States

Application opens: 

Tuesday 11 December 2018

Application deadline: 

Sunday 13 January 2019

Participation: 

First come, first served

Contact: 

Erin Haskell

Registration fee: 

free

Registration closed

Find other similar courses »

Dates additional information: 

This workshop forms part of the Digital Tools and Resources session 2 scheduled from 12:50am until 15:00pm at the Plant and Animal Genomes (PAG) conference. Please see the workshop timetable for further details: https://plan.core-apps.com/pag_2019/event/9441a7255c56cf0ce04b90bfc409bd36

Course Overview

'Exploring your data in Ensembl' will include an overview of how to configure and upload files for browsing in the Ensembl genome browser. 

The Ensembl (www.ensembl.org) and Ensembl Genomes (www.ensemblgenomes.org) projects provide accessible genomic data across the tree of life including vertebrates, bacteria, fungi, metazoa, protists, and plants. We provide annotated genome assemblies, and draw in a range of data from other external databases (e.g. Gene Ontology, Expression Atlas and Reactome) to create a unified database for genome and gene information.

In this session we will show you how you can upload and configure your own experimental data in Ensembl, to aid with analysis. We support upload of a range of file types, including BAM, BED, BigWig and many others. We will demonstrate direct file upload and introduce resources for uploading files by URL, which is necessary for larger file sizes. We will also cover how to search the Track Hub Registry for additional datasets available for display in the Ensembl browsers. We will provide an annotated document with step-by-step details on the processes and sample files that you can access online, and which will remain permanently available after the course.

Audience

Wet-lab researchers and bioinformaticians.

Learning outcomes

At the end of this session participants should be able to:

  • Understand which file types are compatible with the Ensembl genome browser.
  • Where to upload files, and how to configure these in the Ensembl genome browser.
  • How to use CyVerse to create URLs for upload of large files into genome browsers.
  • Browse the trackhub registry for additional, publicly available data tracks.