Tag Archives: Das ENCODE Project Consortium

UCSC Genome Bioinformatics

Video Tipp der Woche: UCSC Genome Browser Exon-only-Modus,en

Das Team von UCSC Genome Browser continues to update their resources and offer new ways to find and visualize features of interest to researchers. One of the newer features is the “Multi-Region” option. When it was first launched, I did a tip on how to use that, with some of the things that I noticed while I was testing it pre-launch. But now the folks at UCSC have their own video on the exon-only display that you might also find useful.

One of the things that is illustrated here is how the exon-only mode is handy to enhance your exploration of RNA-Seq data. It also uses a great ENCODE data set as an example, and if you haven’t been using that collection it’s a good reminder of the kinds of things you can find in that resource still. And this extensive data set shows how much easier it is to look at different isoforms in the data in this new exon-only mode.

So have a look at this display option if you haven’t before, especially how it can help you to see transcript differences. If you aren’t familiar with the ENCODE Daten that’s being used, you can also see our training on that which will help you to understand how to use that data and the filtering features that are also used in this video.

Besonderer Hinweis: I have updated the UCSC Intro slides to include the new Gateway strategies as well. So download those slides for the latest look.

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Bekanntgabe: UCSC Genome Browser tutorials are freely available because UCSC Sponsoren us to do training and outreach on the UCSC Genome Browser.

Quick-Links:

UCSC Genome Browser: http://genome.ucsc.edu

UCSC Genome Browser training materials: http://openhelix.com/ucsc

ENCODE: http://www.openhelix.com/ENCODE2

Referenzen:

Sporn, M., Zweig, A., Rosenbloom, K., Raney, B., Paten, B., Nejad, P., Lee, B., Learned, K., Karolchik, D., RAMspan>, Hinrichs, AS, Hsu, F., Kober, KM, Miller, W., Pedersen, JS, Pohl, A., Raney, BJ , A., Heitner, S., Harte, R., Häußler, M., Guruvadoo, L., Fujita, P., Eisenhart, C., Diekhans, M., Clawson, H., Casper, J., Friseur, G., Haussler, D., Kuhn, R., & Kent, In. (2016). Die UCSC Genome Browser Datenbank: 2016 Update Nucleic Acids Research, 44 (D1) DOI: 10.1093/nar/gkv1275

Das ENCODE Project Consortium (2012). Eine integrierte Enzyklopädie der DNA-Elemente im menschlichen Genom Nature, 489 (7414), 57-74 DOI: 10.1038/nature11247