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blog for posts about Genome Browser tools, features, projects and more.
12 June 2015 -
Have you ever wished that the Table Browser could associate your custom track items
with some other track, while retaining the item names from both? We have released a
new tool that can do just that, and more: the Data Integrator.
Using the Data Integrator you can select up to five tracks, including custom tracks
and hub tracks, and output tab-separated text that contains all the fields from both
the first track and the overlapping items from the other track(s). If you need only
a subset of the fields from your selected tracks, the Data Integrator allows you to
choose which fields to include in the output. You can also query your current Genome
Browser position, search for positions of items such as genes, SNPs, etc. by name,
query over a set of up to 1000 positions, and even retrieve genome-wide data
(subject to data size). The Data Integrator output can be viewed in your web browser
window or downloaded to an optionally gzip-compressed file. Look for "Data Integrator"
in the Genome Browser Tools menu (top blue bar) if you'd like to try it out.
For more information about the Data Integrator's capabilities and usage, see the
As always, we welcome questions and feedback on our public mailing list:
Thanks to Angie Hinrichs and Matthew Speir for all of their work on this feature.
28 May 2015 -
New UCSC Genes Track Released for GRCm38/mm10
We're happy to announce the release of an updated UCSC Genes track for the GRCm38/mm10
mouse Genome Browser. The new release has 63,244 total transcripts, compared with 61,642
in the previous version. The total number of canonical genes has increased from 32,408
to 32,958. Comparing the new gene set with the previous version:
- 59,119 transcripts did not change between versions.
- 55 transcripts were not carried forward to the new version.
- 2,308 transcripts are "compatible" with those in the previous set, meaning
that the two transcripts show consistent splicing. In most cases, the old and new
transcripts differ in the lengths of their UTRs.
- 160 transcripts overlap with those in the previous set, but do not show consistent
splicing (i.e., they contain overlapping introns with differing splice sites).
More details about the new UCSC Genes track can be found on the
UCSC Genes track
Many thanks to Brian Raney and Matthew Speir for their work on this track!
15 May 2015 -
Work for Us! New Job Openings on the UCSC Genome Browser Project:
The UCSC Genome Browser project team is looking for two talented people to join our
engineering staff based in Santa Cruz, CA.
08 April 2015 -
bigGenePred Format Now Supported in the Genome Browser:
We are pleased to announce that the UCSC Genome Browser now supports data in