Fwd: UCSC Newest ENBML version

[Liang, Chun]

---------- Forwarded message ----------

From: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Date: Fri, May 11, 2018 at 11:54 AM
Subject: Re: UCSC Newest ENBML version
To: "Liang, Chun" <lia...@miamioh.edu>
Cc: Lin Liu <li...@miamioh.edu>

Hello Chun,

May I ask that you, please forward your email to gen...@soe.ucsc.edu? This way our entire engineering team will have an opportunity to view your question and other users may also benefit from our answers. Thanks for your understanding in this matter.

Jairo Navarro 

UCSC Genomics Institute

On Fri, May 11, 2018 at 8:48 AM, Liang, Chun <lia...@miamioh.edu> wrote:

Hi, Jairo:

In your test website, we found the newest ENSMBL gene release 92.

(1) http://genome-test.soe.ucsc.edu/cgi-bin/hgTrackUi?db=galGal5&g=ensGene

However, when we downloaded the bed file from your test site, we obtained the same old file as release 89. 

(2) http://genome-test.soe.ucsc.edu/cgi-bin/hgTables

I want to double check with you that in your test site, the data downloaded from (2) is also consistent with (1) in terms of ENSEMBL version. Am I correct?

Thank you very much for your attention. 

Chun Liang, PhD

Professor

Department of Biology

Miami University

Oxford, Ohio 45056

Web site: http://bioinfolab.miamioh.edu

Phone: 513 529 2336

Email: lia...@miamioh.edu

[Matthew Speir]

Hello, Chun.

Thank you for your question about updates to the Ensembl Genes tracks in the UCSC Genome Browser. 

You can read more about Ensembl's release process here: https://www.biostars.org/p/69653/. In short, gene annotations may not change at all from release to release.

I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir

UCSC Genome Bioinformatics Group

Training videos & resources: http://genome.ucsc.edu/training/index.html

Want to share the Browser with colleagues?

Host a workshop: http://bit.ly/ucscTraining

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Matthew Speir

Outreach, User Experience, Quality Assurance and User Support

HCA, CIRM, and UCSC Genome Browser

UCSC Genomics Institute