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So Many Tools!

There are lots of tools in each genome browser. We encourage you to explore them with your own data. Here are some highlights:

  • Ensembl's Variant Effect Predictor (Ve!p) - upload a VCF and get an overview of the numbers and consequences of variants (based on known annotations) in your file. It doesn't replace more in-depth analyses using more robust computational tools, but it is a good way to see a graphical summary of your variants, so you can make decisions on how to clean up your VCF files, if necessary.
    • The rough equivalent in UCSC is the Variant Annotation Integrator, which gives you more options on what to do with your files, but is less user-friendly. It gives you files in Variant Effect Predictor format, though, so you can take those files over to Ensembl for visualization.
  • LiftOver tools - allow you to convert between older genomes (eg. hg19) to current (eg. hg38) or other builds. Availalbe from the Tools menu in both browsers.
  • Gene Interactions from UCSC. More of a fun tool, it provides simple network maps of your chosen gene. Also available from the Tools menu.
  • Linkage Disquilibrium Calculator from Ensembl. Requires a little bit of pre-work to prepare files with lists of regions or variants, but allows you to select any number of populations from 1000 Genomes or GGVP data. Available from Ensembl's Tools menu.

There are more tools from each site, and more are being created all the time.

Uploading Your Own Data

Both sites allow you to upload your own experimental data. There isn't time to demonstrate this for this session, but we have included instructions on how to prepare data for upload to UCSC using Globus and Quest. Those instructions, created by NUIT Research Computing and Data Services, are available in this repository. These instructions can be modified to work for Ensembl, too.

Uploading data can be done in the My Data menu in UCSC, and the Custom Tracks menu in the browser view of Ensembl.

Watch this YouTube video by Elizabeth Bartom!

Elizabeth is the Scientific Associate Director of Bioinformatics at the Lurie Cancer Center. She has created a very easy-to-follow seminar on uploading your own data to UCSC:
The UCSC Genome Browser: Exploring Your Sequencing Data