A Korean ENCODE adventure

Working as an Outreach Officer for Ensembl means lots of exciting adventures around the world to teach Ensembl to local scientists. Last month I was privileged to be able to travel to South Korea to give an ENCODE workshop with Bob Kuhn from UCSC.

Bob and me, with our Korean hosts
Bob and me, with our Korean hosts

The participants were interested to learn about how Ensembl and UCSC use genome assemblies from projects like the Genome Reference Consortium. It was clear that many people had not realised the extent of the work that goes into producing a genome assembly, by sequencing the genome in contigs then putting them back together (learn more in this video). Or how errors in the human genome are dealt with using patches. I was able to explain to them how Ensembl works together with groups like Havana to produce the genes for the trusted GENCODE gene sets for human and mouse, and how they could find out about these genes in Ensembl.

Even more excitingly, I got to preview some new data. The Ensembl regulation team gave me access to their new regulatory build track hub, which you can learn more about in Daniel Zerbino’s blog post. I was able to show off how Ensembl bring together and process the raw ChIP-seq data from ENCODE and other sources to try to identify where regulatory features might be on a genome-wide scale, and the activities of those features. It was exciting to be able to preview something new for the workshop participants, and their feedback suggests that the new regulatory build is going to be a hit.

Bob showed off the UCSC genome browser in the same workshop, and we worked together well. Though we have competing browsers, we’re really on the same team: the team that believes high quality genomic data and tools should be available to all and works hard to provide that. We can learn from each other to provide the best way of giving our users the data and analyses they need.

My next stop is the Open Door Workshop in Uruguay. Don’t forget, you can host a workshop at your institute to learn the basics of using Ensembl, and to find out about the latest Ensembl functionality and what’s coming with the new human assembly.

Comments are closed.