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12 August 2015 New blog post: How to share your UCSC screenthoughts

Do you want to save your UCSC Browser screenthoughts, or share them with a colleague, or make a slide for a talk, or publish them in a paper? Saving the state of your screen can take two forms: static or dynamic. You can snap and save a picture of the screen, or you can share a link to an active Genome Browser. We talk about both approaches here and discuss some of the advantages and pitfalls of each.

29 June 2015 GENCODE Genes Now the Default Gene Set on the Human (GRCh38/hg38) Assembly

In a move towards standardizing on a common gene set within the bioinformatics community, UCSC has made the decision to adopt the GENCODE set of gene models as our default gene set on the human genome assembly. Today we have released the GENCODE v22 comprehensive gene set as our default gene set on human genome assembly GRCh38 (hg38), replacing the previous default UCSC Genes set generated by UCSC. To facilitate this transition, the new gene set employs the same familiar UCSC Genes schema, using nearly all the same table names and fields that have appeared in earlier versions of the UCSC set.

By default, the browser displays only the transcripts tagged as "basic" by the GENCODE Consortium. These may be found in the track labeled "GENCODE Basic" in the Genes and Gene Predictions track group. However, all the transcripts in the GENCODE comprehensive set are present in the tables, and may be viewed by adjusting the track configuration settings for the All GENCODE super-track. The most recent version of the UCSC-generated genes can still be accessed in the track "Old UCSC Genes".

The new release has 195,178 total transcripts, compared with 104,178 in the previous version. The total number of canonical genes has increased from 48,424 to 49,534. Comparing the new gene set with the previous version:

More details about the new GENCODE Basic track can be found on the GENCODE Basic track description page.

26 June 2015 New Bonobo (panPan1) Assembly Now Available in the Genome Browser: We are pleased to announce the release of a Genome Browser for the May 2012 assembly of bonobo, Pan paniscus (Max-Planck Institute panpan1, UCSC version panPan1). Read more.

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