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15 June 2016 - New Official Asian Mirror Released
We are pleased to announce the introduction of a new supported Genome Browser mirror
to serve our users in Asia. The genome-asia server
which is administered by UCSC, is physically located at the
RIKEN Yokohama Campus
Genome-asia is intended as an alternate, faster access point for those Browser users
who are geographically closer to Asia than to the western United States. The mirror
is functionally identical to the U.S.-based server, with one exception. Custom tracks
residing on the U.S. server are not automatically accessible from the genome-asia mirror;
therefore, the use of these custom tracks and saved sessions containing them will require
some manual intervention.
Genome Browser users located in Asia will be automatically redirected to genome-asia
when they click the "Genomes" menu item on the Genome Browser home page, but will have
the option to remain on the U.S.-based server. In addition to the
genome-asia mirror, we continue to support a Europe-based Genome Browser mirror
in Bielefeld, Germany. A third-party mirror in
is available as an emergency backup in the rare event
that our three supported sites are offline.
We wish to express our special thanks to Dr. Hideya Kawaji at the
Center for Computing and Communication for making this possible. We would also
like to acknowledge the following members of the UCSC Genome Browser team for their efforts:
Galt Barber, Robert Kuhn, Jorge Garcia, and Luvina Guruvadoo.
6 June 2016 - New video: Exon-only mode
We are pleased to announce the release to our YouTube channel of a new
in which we demonstrate the recently released Multi-Region feature in
exon-only mode. This feature is useful for those studying gene expression or
undertaking whole-exome sequencing. By removing intronic and intergenic regions,
exon-only mode shows the portion (sometimes as little as a few percent) of the
genome most useful for these analyses.
This video is
to allow easy access to relevant sections and comes with a transcript for the
Thanks to Robert Kuhn and David Gibson for production.
1 June 2016 - New Density Graph Feature!
The Genome Browser is proud to announce a new "density graph" feature for
a variety of tracks, including BAM custom tracks, that converts data into a summary display.
The density graph feature enables certain track types to be displayed as a bar graph where
the height is proportional to the number of reads mapped to each genomic position.
Through dynamic calculation of items in the current window, this feature plots a line
similar to a wiggle graph that can be customized with a number of
graph-based configuration options such as drawing indicator lines,
smoothing plots, adjusting graph height and vertical range, and switching from bars to
points. Please note that the feature is best displayed with Display mode set to full
and that the default is auto-scale data to view. Please note that using this
feature on a virtual machine Genome Browser in a Box (GBiB) may benefit from
To turn on the feature click into the track controls for certain track types,
such as a BAM custom track, and check the box next to "Display data as a
density graph" to see graph configurations and then click "Submit".
To see the new density graph feature in use, please see this example
Thanks to Brian Raney for the implementation of this feature.
10 May 2016 - New Gateway Page!:
The UCSC Genome Browser team is proud to announce a newly redesigned
Genome Browser Gateway page.
Please see our Gateway video for an introduction to these new features.