Tag Archives: custom tracks

UCSC Genome Browser: New Euro server (affects custom tracks)

So there’s some news from the UCSC Genome Browser team. It’s great news for a better user experience–sharing the load on different continents. But the first thing I wondered about when I heard that was: what about sessions and custom tracks?

We tell people in trainings that they can share their sessions with colleagues around the world by sending a link. But now that link behaves a bit differently depending on where you are–I’m told that if I got a custom track session link from a European server user, I’d get directed to that one. So keep that in mind, and note that you might have to tweak things just a bit.

Whole announcement email from the UCSC announcement list:

The UCSC Genome Browser is pleased to announce the introduction
of a new mirror site to serve our users in Europe.  Genome-euro is an
official European mirror site of the UCSC Genome Browser, at
http://genome-euro.ucsc.edu. The server is physically located at the
Universität Bielefeld Center for Biotechnology in Bielefeld, Germany,
and is administered by UCSC.   Genome-euro is meant to be an alternate,
faster access point for those Browser users who are geographically
closer to central Europe than to the western United States.

All functionality will be the same as on the US server, although Custom
Tracks will not be transferred. Saved Sessions containing Custom Tracks
will require some manual intervention

When European users navigate to the US server home page and click
the “Genomes” menu item, they will receive a notification that they have
been redirected to the more geographically-appropriate server. They will
have the option to remain on the US server, as  described in our
documentation

The backup mirror in Aarhus, Denmark will continue to serve as a
emergency site in the event of the official sites in California and Germany
malfunctioning.

Thanks to Steve Heitner, Brooke Rhead, Galt Barber, Hiram Clawsen,
Jorge Garcia and the rest of the Genome Browser staff for engineering
and testing.

We wish to express our special thanks to our colleagues at the
Universität Bielefeld Bioinformatics, especially Jens Stoye, for making
this possible.

Regards,

–b0b kuhn
ucsc genome bioinformatics group

If you don’t know what I’m talking about with sessions and custom tracks, be sure to see our introductory and advanced tutorials that covers those aspects.

Video Tip of the Week: Track Hubs in UCSC Genome Browser


Today’s tip of the week introduces a new feature at the UCSC Genome Browser which we will be adding to our UCSC Genome Browser and UCSC Table Browser tutorials (both free) soon: Track Hubs. Track Hubs are annotation tracks for very large datasets housed at non-UCSC servers that might not be conducive for the custom track utility to manage.

Research groups will be able to create their own track hubs of large datasets for search and viewing. They can also register their tracks hubs with UCSC so that they may be used by the public. Users of the genome browser will be able to load those annotation tracks to the genome and table browsers for viewing and searching. The user guide for viewing, creating and registering track hubs is here.d

Today’s tip takes you on a quick tour to show you how to load and view track hubs using one of the two currently available ones from Washington University of epigenomics data.

Now, as a user, if you don’t find the data you need in the native tracks at UCSC, you have two additional places to look, the custom tracks shared by many users here and the track hubs of larger datasets.

 

 

 

New custom track type at UCSC Genome Browser

Just a quick note about a new type of custom track supported on the UCSC Genome Browser.  We get a lot of questions about support for the next-gen sequencing types of data peeople are generating or expect to be generating soon.  This came across the announcement mailing list yesterday.  It also includes some helpful links for more details about this track and about other large data set track types.

We are pleased to announce the availability of another new track type for Custom Tracks: the Binary Alignment/Map (BAM).

BAM is the compressed binary version of the Sequence Alignment/Map (SAM) format, a compact and index-able representation of nucleotide sequence alignments. Many next-generation sequencing and analysis tools work with SAM/BAM. For custom track display, the main advantage of indexed BAM over PSL and other human-readable alignment formats is that only the portions of the files needed to display a particular region are transferred to UCSC. This makes it possible
to display alignments from files that are so large that the connection to UCSC would time out when attempting to upload the whole file to UCSC. Both the BAM file and its associated index file remain on your web-accessible server (http or ftp), not on the UCSC server. UCSC temporarily caches the accessed portions of the files to speed up interactive display.

Read more about the BAM file type here: http://genome.ucsc.edu/goldenPath/help/bam.html

Read more about the SAM project here: http://samtools.sourceforge.net/

For help with samtools, please contact the SAM tools mailing list:
http://sourceforge.net/mail/?group_id=246254

Read more about other file types available for use in the genome browser for very large data sets:
https://lists.soe.ucsc.edu/pipermail/genome-announce/2009-July/000165.html

"Research news gives biologist a heart attack"

The GenomeWeb blog had a “This week in Genome News” post that lead with:

In Genome Biology this week, scientists at the University of Rochester studied the evolution of R1 and R2 retrotransposons across 12 Drosophila genomes. These specifically insert into the 28S rRNA genes. They found that most copies of R1 and R2 in each species were found to exhibit less than 0.2% sequence divergence, suggesting that all copies are relatively new. In looking at target DNA cleavage and synthesis, they found that each active element generates its own independent lineage and that both R1 and R2 use “imprecise, rapidly evolving mechanisms” for second strand synthesis.

I read it wrong. I thought it said that there was less than 0.2% difference in copies _between_ species. I had a minor heart attack. Why?

Continue reading

SNPedia on the HapMap GBrowser

SNPs are hot. Everywhere we go for training people want to see SNPs. SNPs from many sources. And we know a lot of places to find them. Although everything gets in to dbSNP, of course, sometimes it helps to look at subsets of SNPs that were the focus of special projects. For example, the genes and SNPs from WashU in the SeattleSNPs project are focused on inflammation. If your genes are on their list, you are golden–you can look at the gene of interest in deep detail. Same for the NIEHS SNPs–those genes and SNPs are environmentally influenced.

Other projects are broader. Of course, the HapMap project identified millions of SNPs in various populations. And they did this genome-wide. The HapMap folks created a browser to focus on their data–but viewed on the official genomic sequence. That browser is based on the GBrowse software, which many people have used to create views of their favorite genomes and data.

Sometimes you can take the SNPs from one project, and load them onto another place to look at them. In the case of SeattleSNPs, you can find any gene page and click to load those SNPs as custom tracks on to the UCSC Genome Browser by clicking the “Golden Path” links in the middle of the page.

I was just looking today at another source of SNP data that you can load into a viewer. SNPedia is a resource that collects SNP information. I just found out today on the SNPedia blog that you can view those SNPs right on the HapMap browser–it is so easy! There are 2 URLs for the SNPedia data (http://www.snpedia.com/files/gbrowse/snpedia and http://www.snpedia.com/files/gbrowse/microarrays, you can see more info about them on their blog). All you have to do is:

  • go to the HapMap browser (sample location from the SNPedia blog)
  • go down to the very bottom of the HapMap page
  • paste each of those SNPedia URLs in the “Add remote annotations:” section one at a time. Click the Update URLs button each time.
  • and the data gets loaded from SNPedia right on to the HapMap browser.

So you get the genomic context, the HapMap context, and the SNPedia data too. I clicked one of the ones in this view (rs7901695) and it took me back to the SNPedia page for that SNP–which links back to a GeneSherpas blog post. Isn’t it amazing what you can learn from blogs?