This week’s video tip demonstrates a new feature at the UCSC Genome Browser. I think it’s kind of unusual, and conceptually took me a little while to get used to when I started testing it. So I wanted to go over the basics for you, and give you a couple of tips on things that I had to grok as I got used to this new visualization option.
La headline for the news item describes it as: “Combine Multiple Regions of the Genome Browser into a Single Visualization!” y
Have you ever wished you could remove all of the intronic or intergenic regions from the Genome Browser display? Have you ever dreamed of being able to visualize multiple far-flung regions of a genome? Bueno, now you can with the new “multi-region” option in the Genome Browser!
I should probably start with the first thing that confused me–the name “multi-region”. I thought that I was going to be able to see maybe part of a region on chromosome 1, and something on chromosome 8, maybe at the same time. But that’s not how this works. En este caso, you look at multiple regions along the same chromosome, with some of the intervening sequences snipped out. This creates a sort of “virtual chromosome” for you to interact with.
En el video de esta semana, I’ll show you how that looks using the BRCA1 gene. First I show how you can look at all the exons together–with introns clipped out. And then I show how you can see the genes in the neighborhood displayed together, with the non-coding regions clipped out. These are 2 of the separate options for viewing.
Yo uso el “Ver” menu option to illustrate this feature. But there is another way to access it–you can use the “multi-region” button in the browser buttons area.
To keep the video short, I didn’t go into every detail on this tool. Usted debe revisar la news announcement for it, and the link to the additional details in the User Guide documentation para más. The new feature is also mentioned briefly in the lastest NAR paper on the UCSC Genome Browser (relacionados a continuación). And you should try it out, por supuesto! That’s the best way to really understand how it might help you to visualize regions of the genome that you might be interested in.
Also as in the news, thanks to the development team. I am always looking for new visualizations, and this fun to test!
Thank you to Galt Barber, Mateo Speir, and the entire UCSC Genome Browser quality assurance team for all of their efforts in creating these exciting new display modes.
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— UCSC Genome Browser (@ GenomeBrowser) De marzo 9, 2016
UCSC Genome Browser: genome.ucsc.edu
News item on multi-region: http://genome.ucsc.edu/goldenPath/newsarch.html#030816
Training materials on the UCSC Genome Browser: http://openhelix.com/ucsc
Espolón, M., Rama, A., Rosenbloom, K., Raney, B., Patrocinadores, B., Nejad, P., Sotavento, B., Aprendido, K., Karolchik, D., Hinrichs, A., Heitner, S., Duro, R., Haeussler, M., Guruvadoo, L., Fujita, P., Eisenhart, C., Diekhans, M., Clawson, H., Casper, J., Peluquero, G., Haussler, D., Kuhn, R., & Kent, En. (2016). La UCSC Genome Browser base de datos: 2016 actualización Nucleic Acids Research, 44 (D1) DOI: 10.1093/nar/gkv1275
Revelación: UCSC Genome Browser tutorials are freely available because UCSC patrocinadores us to do training and outreach on the UCSC Genome Browser.