Tag Archives: UCSC Table Browser

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Video Tip of the Week: Send UCSC Genome Browser sequence to external tools

The folks at the UCSC Genome Browser are always adding new features, new data, and new genomes to their site. And although they use the genome-announce mailing list to get the word out, even I can miss a notice. There was news recently of a new feature associated with the graphical genome browser that I’ve been waiting for (as I had tested it prior to roll-out), but they sent the email out when I was prepping for Thanksgiving, and I didn’t catch it for a few days.

But now I’ve had a chance to see it, kick the tires more, and I want to show you how it works. The basic feature is this: you can take the genomic sequence from the window you are viewing and with a couple of clicks deliver it right to another tool for more helpful data or analysis. This is really handy from the graphical viewer. Before you were limited to obtaining the sequence with the “Get DNA” option. You could get the sequence, copy/paste, and do whatever. Which is fine, and might still be right for some other tools. But now you can skip that copy/paste part and explore features of your sequence directly. If you don’t have time for the video, here’s the bullet–use this View–>In External Tools menu to get there.

View External Tools

There are a range of options. You can still jump right to NCBI Map Viewer or Ensembl to look at the same region in their browsers. But now you can select primers, see restriction sites, look at RNA characteristics, find protein domains, or examine CRISPR tools. You can look for transcription start sites or some TF binding motifs. Here’s this week’s Video Tip that shows the process.

You can still “get DNA” if you want to. And you can still use the Table Browser to send data from your custom queries to even more tools (like Galaxy and others). But we know from our workshops that most people we train spend their time in the graphic browser and these tools should help them accomplish more. You can see all of these options in our freely available training suites (linked below).

To see if there are other things you missed over the past year, check out the new NAR database issue paper from the UCSC team (linked below). It has updates about many of their accomplishments and recent features, so have a look and see if there are other useful aspects for assisting your research.

Quick links:

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

Intro full training suite: http://openhelix.com/ucsc

Advanced topics training suite: http://openhelix.com/ucscadv

Reference:

Speir, M., Zweig, A., Rosenbloom, K., Raney, B., Paten, B., Nejad, P., Lee, B., Learned, K., Karolchik, D., Hinrichs, A., Heitner, S., Harte, R., Haeussler, M., Guruvadoo, L., Fujita, P., Eisenhart, C., Diekhans, M., Clawson, H., Casper, J., Barber, G., Haussler, D., Kuhn, R., & Kent, W. (2015). The UCSC Genome Browser database: 2016 update Nucleic Acids Research DOI: 10.1093/nar/gkv1275

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

Video Tip of the Week: InterMine for complex queries

We’ve been fans of InterMine for a long time. We did a tip-of-the-week in a while ago that highlighted ways that this software can be used to mine from big data projects of many types. The generic framework of InterMine can be customized for use at different projects–today I’ll include videos from the FlyMine installation and the YeastMine flavor–but you may find versions of this handy tool in many other places as well.

The first video is a broader overview of different types of things you can do–and although this is FlyMine, you’ll find similar behavior at the other Mines too.

This next video is more specific about a task that people need to accomplish–working with a list of genes. This example was recently produced by the YeastMine folks, but again this should work in a similar way across other Mines. You should also read the SGD blog post on it–Create, Analyze, Save: the Power of Gene Lists in YeastMine.

The other thing that I noticed about this framework is the effort of several of these model organism Mines to coordinate into this InterMOD structure. Although I am often wary of “one search to rule them all” sorts of efforts, there can be value in this as a central organizing principle as we keep adding more species genomes that may not have as well-developed communities and infrastructure to support them.

I certainly use a lot of query tools that are similar to these–like the UCSC Table Browser, and BioMartUniProt offers ways to build queries that’s different but conceptually similar. Using these interfaces you can construct some clever and complex ways to extract information out of data repositories.

Quick links:

InterMine: http://intermine.github.io/intermine.org/

FlyMine: http://www.flymine.org/

YeastMine: http://yeastmine.yeastgenome.org/

InterMOD: http://intermod.intermine.org

References:

Smith R.N., Aleksic J., Butano D., Carr A., Contrino S., Hu F., Lyne M., Lyne R., Kalderimis A. & Rutherford K. & (2012). InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data., Bioinformatics (Oxford, England), DOI:

Lyne R., Smith R., Rutherford K., Wakeling M., Varley A., Guillier F., Janssens H., Ji W., Mclaren P. & North P. & (2012). FlyMine: an integrated database for Drosophila and Anopheles genomics., Genome biology, PMID:

Balakrishnan R., Park J., Karra K., Hitz B.C., Binkley G., Hong E.L., Sullivan J., Micklem G. & Cherry J.M. (2012). YeastMine–an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit., Database : the journal of biological databases and curation, PMID:

Sullivan J., Karra K., Moxon S.A.T., Vallejos A., Motenko H., Wong J.D., Aleksic J., Balakrishnan R., Binkley G. & Harris T. & (2013). InterMOD: integrated data and tools for the unification of model organism research., Scientific reports, 3 (1802) PMID:

Video Tip of the Week: GenomeSpace, an integrator of integrators


Recently, the Broad Institute announced a new tool: GenomeSpace. When I first looked at it, admittedly a very cursory look, I wasn’t sure how it would be much different than an integrator of tools like Galaxy or GenePattern. Obviously that cursory look was wrong at first glance since both Galaxy and GenePattern are in their list of tools that are supported. So what is GenomeSpace? Well, you can read the answer here at their “What is GenomeSpace” page :). Basically, GenomeSpace has several functions. As described here, “GenomeSpace supports several bioinformatics tools, all integrated to allow easy accessibility, easy conversion, and frictionless sharing.” It is a space (in that every expanding Amazon cloud) that allows you to store your data files and, importantly, GenomeSpace allows you to seamlessly move those files between the tools to complete complex, or simple, analyses. It achieves this by automatically converting file formats and by allowing the user to attach their accounts at the tools to their account at GenomeSpace, thus alleviating the need to log in several times when using more than one tool.

To get a good idea of what GenomeSpace might be able to do for a researcher, check out the recipes on the site. As Anton  states:

GenomeSpace is an integration of integrators,” Nekrutenko said. “The benefit to the user is that this brings together distinctive collections of functionalities offered by individual tools.”

The site is new, and only in beta. They only recently opened up registration from their invite-only stage. As such, there are some bugs and some features that aren’t quite at full capacity. For example, the Galaxy and UCSC Table Browser integration is with the test versions of those tools during beta. Thus, for example, your account at Galaxy will not be recognized when trying to link that account with GenomeSpace. I had to create a new one on the test site. And, if you go to the public version of the Table Browser, it will look different (no link to GenomeSpace as there is on the test site). Currently there are seven tools, more to come.

All that aside, it’s definitely a tool to get acquainted with. And with that in mind, take a quick introductory spin with me in this week’s video tip to get an idea of what you might be able to do.

Quick Links:

GenomeSpace
UCSC Table Browser (OH tutorial)
Galaxy (OH Tutorial)
Cytoscape (OH Tutorial)
Genomica
GenePattern
IGV
InSilicoDB

Broad Institute
NHGRI 

 

UCSC Table Browser webinar follow-up post (May 24)

We’ll be having our May 24th webinar today, and we find there are questions to follow up afterwards that are often better handled in discussions on the blog.

If there are questions we didn’t have time to get to–or things we want to expand on with more detail–we can discuss them in this thread.

Or if you have other things you’ve been meaning to ask, let us know.

If you can’t make the webinar, the same material is covered in the training movie, slides, and exercises that are freely available, sponsored by the UCSC team: http://www.openhelix.com/ucscadv. You can also sign up to be informed of future webinars coming up on these topics, Galaxy, ENCODE and others.

Webinars on how to use UCSC Genome and Table browsers

As we have in the past, we are offering free webinars in the coming weeks on the UCSC Genome Browser and Advanced discovery using the Table Browser and custom tracks. These have been quite popular in the past, so sign up soon!

The Intro to the Genome Browser webinar will be Thursday, May 17th at 10am Pacific time (1pm ET). Check here for your time zone.

The Table Browser and custom tracks webinar will be Thursday, May 24th at 10am Pacific time (1pm ET). Check here for your time zone.

You can register here for the UCSC Genome Browser Intro and register separately here for the Table Browser and custom tracks webinar. You’ll need to register at OpenHelix if you haven’t already. It’s free and you’ll get no emails from us unless you opt in to our most excellent newsletter  or ask to be notified of future webinars :D. Registration and attendance are free.

We have several months of free webinars planned including on ENCODE, Galaxy, PDB  and others. Keep tabs with us here or on the webinars page (or though email notification) to be notified when those free webinars are coming.