49dd3ac0e030676ecf09c80494f5a652352a7520 brianlee Thu Jun 30 16:00:34 2016 -0700 Adding hgCustom.c links to new track formats refs #14717 diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index b691a47..21cc401 100755 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,237 +1,237 @@

News

To receive announcements of new genome assembly releases, new software features, updates and training seminars by email, subscribe to the genome-announce mailing list. Please see our blog for posts about Genome Browser tools, features, projects and more.

- 30 June 2016 - CRAM Files now supported! + 30 June 2016 - CRAM Files Now Supported!

We are excited to announce the support of CRAM files on the Browser! Read more here.

See complete details on the CRAM Track Format page. To load an example CRAM file from the 1000 Genomes Project where reads are displayed as a bar graph using the "Display data as a density graph" option, click here.

Thanks to Jonathan Casper and Brian Raney for the implementation of this feature.

30 June 2016 - Updated Gene Tracks Available for the Human (hg38) and Mouse (mm10) Assemblies

We are pleased to announce the release of an updated GENCODE Genes track for the Human (GRCh38/hg38) assembly. The GENCODE v24 gene set has 197,782 total transcripts, compared with 195,178 in the previous version. The total number of canonical genes has increased from 49,534 to 49,948. Comparing the new gene set with the previous version:

193,647 transcripts did not change.
128 transcripts were not carried forward to the new version.
997 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.
406 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 GENCODE Genes track can be found on the GENCODE v24 track description page.

Many thanks to Brian Raney and Luvina Guruvadoo for their work on this track!

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We are pleased to announce the release of an updated UCSC Genes track for the Mouse (GRCm38/mm10) assembly. The new release has 63,759 total transcripts, compared with 63,244 in the previous version. The total number of canonical genes has increased from 32,958 to 33,079. Comparing the new gene set with the previous version:

60,827 transcripts did not change between versions.
148 transcripts were not carried forward to the new version.
1,929 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.
340 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 description page.

Many thanks to Jonathan Casper and Christopher Lee for their work on this track!

27 June 2016 - New Way to Share Sessions - Public Sessions!

We are excited to announce the release of the Public Sessions page, the newest way to share your UCSC Genome Browser snapshots with your colleagues and the world. The Public Sessions page collects sessions that users have elected to share publicly. Sessions on this page can be filtered based on assembly, name, or a phrase from the description. Sessions can also be sorted based on their popularity or creation date. To add your own sessions to this Public Sessions page, just check the box under "post in public listing" on the session management page.

The Genome Browser session management page has also received an update with the release of the new Public Sessions page. Sessions are now arranged in a table, where varying numbers of sessions can be displayed on a page of this table. Sessions can now be filtered and ordered based on session name, primary assembly, and creation date. Clicking on the session name now displays that session in the Genome Browser. Session details, such as the name or the description, can be changed using the "details" button in the new table layout.

The release of the new Public Sessions page also marks a change in our session expiration policy. We no longer expire sessions and associated custom tracks four months after their last use. Please note, however, that the UCSC Genome Browser is not a data storage service and that we encourage you to keep local copies of your session contents and custom track data.

For more information about using sessions to share snapshots of the UCSC Genome Browser, please see the User Guide or our blog post, "How to share your UCSC screenthoughts."

Thanks to Jonathan Casper and Matthew Speir for their work on this new tool.

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 (http://genome-asia.ucsc.edu), which is administered by UCSC, is physically located at the RIKEN Yokohama Campus in Japan.

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 (http://genome-euro.ucsc.edu) in Bielefeld, Germany. A third-party mirror in Aarhus, Denmark, 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 RIKEN Advanced 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 proud to announce a new video demonstrating the exon-only feature. This feature is useful in gene-expresson studies and for those doing whole-exome sequencing. Read more.

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. Read more.