Ensemble transcripts data for Hg38-unavailable

[Genetics Savvy]

Hello,

In the table browser (http://genome.ucsc.edu/cgi-bin/hgTables?command=start),

I wanted to download genes and gene predictions data for human genome assembly GRCh38/hg38, I was unable to find track for Ensembl genes. 
When would this track/data be added to be available for download?

Or, if you could provide me any link to download the same.

Attaching the screenshots for hg19 and hg38.PFA.

Much thanks.

genetic...@gmail.com

[Brian Lee]

Dear Savvy,

Thank you for using the UCSC Genome Browser and your question about Ensembl genes for hg38. The data you are looking for can be found on the GENCODE track selection.

If you navigate to the GENCODE track page, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=wgEncodeGencodeCompV22 , you will see the following note: "As of GENCODE Version 11, Ensembl and GENCODE have converged. The gene annotations in the GENCODE comprehensive set are the same as the corresponding Ensembl release." For hg38, you should be able to obtain the desired output from the wgEncodeGencodeCompV22 table under All GENCODE v22.

On the hg19 assembly the Ensembl track was maintained, but with the hg38 release, this has been discontinued. To help exemplify this similarity here is the hg19 Ensembl v75 track displayed next to the corresponding hg19 v19 GENCODE release (http://www.gencodegenes.org/releases/):

http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Brian%20Lee&hgS_otherUserSessionName=hg19.Ensembl.v75.GENCODE.v19

Data is also available from download on our Download server. If you click "Downloads" on the left hand side of our homepage, http://genome.ucsc.edu/, you can then navigate to the Human "Annotation database" link for hg38, and find the wgEncodeGencodeCompV22.sql and wgEncodeGencodeCompV22.txt.gz files: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UCSC Genomics Institute

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