UCSC Genome Bioinformatics

Video Tip of the Week: UCSC Genome Browser Exon-only Mode

… 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 …


Video Tip of the Week: New UCSC Genome Browser Gateway look

… been a lot of change over the years–so much more data, so many new tools, new species. All that ENCODE information and a portal for that. But the look of the main site was largely the same. Here’s a post we did that included the UCSC site traffic in 2000, and another time we took a look at the old style interface ~2004. And there was the switch to t he new blue look in 2012.

However, the main gateway page was largely the familiar look. The gateway–where you begin to do most …

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Video Tips of the Week, Annual Review 2015. Part II

… variation browsing

August 26:  Human Metabolome Database, HMDB


September 2: ENCODE Data Coordination Center, phase 3

September 9: UCSC features for ENCODE data utilization

September 16: BANDAGE for visualization of de novo assembly graphs

September 23:  UCSC Xena System for functional and cancer genomics

September 30: Global Biotic Interactions database, GloBI


October 7: Weave, Web-based Analysis and Visualization Environment

October 14: …

Grinstein on dataviz at VIZBI.

Video Tip of the Week: Weave, Web-based Analysis and Visualization Environment

… Desktop and ran it on my little system. I grabbed some transcription factor score data from the ENCODE project with the UCSC Table Browser, got it in csv format, pulled it in, and within seconds was looking over all the data on the X chromosome for this TFBS I was interested in. Clicking an item in my table highlighted it in my histogram. And that was just to kick the tires. According to the video, you could have had a tile of Cytoscape (because you can integrate with Cytoscape–I …

UCSC Genome Bioinformatics

Video Tip of the Week: UCSC features for ENCODE data utilization

As noted in last week’s tip about the ENCODE DCC at Stanford, there was a workshop recently for the ENCODE project. There were a lot of folks speaking and a big room full of attendees. You should check out the full agenda and the playlist at the NHGRI site for all the videos, slides, and handouts:  ENCODE 2015: Research Applications and Users Meeting.

This week I’m highlighting another video from this event. In this one, …


Video Tip of the Week: ENCODE Data Coordination Center, phase 3

Image via: A User’s Guide to the Encyclopedia of DNA Elements (ENCODE). doi:10.1371/journal.pbio.1001046.g001

The ENCODE project began many years ago, with a pilot phase, that examined just 1% of the human genome. But this initial exploration helped the consortium participants to iron out some of the directions for later stages–including focusing on specific cell lines, techniques, and technologies in Phase 2. There have been a number of publications …

Video Tip of the Week: TargetMine, Data Warehouse for Drug Discovery

… for different topics when that’s possible, rather than building a whole new system. There are ModENCODE, rat, yeast mines, and more. This week’s tip is about one of those others– TargetMine is built on the InterMine foundation, with a specific focus on prioritizing candidate genes for pharmaceutical interventions. From their site overview, I’ll add this description they use:

TargetMine is an integrated data warehouse system which has been primarily developed for the purpose …

Video Tip of the Week: Biodalliance browser with HiSeq X-Ten data

… here: Catalog ID: GM12878. Conveniently, this is one of the Tier 1 cell lines from the ENCODE project too, so there is other public data out there on this cell line–which I have explored in the past and knew some things about.

There are 2 different data sets of the sequence in the download files, and one of them is available in the browser to view. I’m sure the Genoscenti will be all over the downloadable files. But because I’m always interested new visualizations, I …

Video Tip of the Week: New UCSC “stacked” wiggle track view

… we don’t always have time to go into the details of this view, although we do explore it in the ENCODE material, because the track I’m using is one of the ENCODE data sets. I’ll use the same track in the same region as the announcement, which is shown here:

But when I first looked at this, I wasn’t sure if the peak–focus on the pink peak that represents the NHLF cell line–was meant to cover the whole area underneath or not. What I was trying to figure out is essentially this …