refseq summary option

[Patrick Koty]

For the last week or so I am unable to select the option for refseq summary.

 

Tools>table browser> I used to be able to select track: RefSeq Genes, region: position, output format: selected fields> get output

Then I was able to check Name2 from select fields and RefSeq summary from linked tables and then allow selection but it no longer has the option to check refseq summary

 

How can I get this functionality back.

 

Pat

 

Patrick P. Koty, Ph.D., FACMG

Section Head, Medical Genetics

Professor of Pediatrics and Pathology

Director, Clinical Molecular Genetics Laboratory

Co-Director, Clinical Cytogenetics and Molecular Cytogenetics Laboratories

Medical Center Boulevard

G24 NRC Building

Winston-Salem, North Carolina 27157

 

Telephone: 336-713-7579

Fax: 336-713-7577

Email: pk...@wakehealth.edu

 

 

[Brian Lee]

Dear Patrick,

Thank you for your question about the RefSeq Genes track disappearing in the Table Browser.

We have recently moved the track into a composite (a collection of tracks) along with many other new NCBI data tracks, as noted in this announcement: http://genome.ucsc.edu/goldenPath/newsarch.html#040418

We are sorry this caused any confusion, it does mean that people are not finding the track where they were expecting the track in the previous location, but a few clicks can return the track.

The old track should still function the same way and the data should be available, please let us know if you experience any issues with the new set of tracks. To turn on the track you can click into the composite titled "NCBI RefSeq" and then select the older "UCSC RefSeq" that you were previously using, or chose from one of the new NCBI RefSeq tracks. More details about these tracks, their construction, and how to access their underlying data can be found on this blog post that explains when we made this change for other assemblies in the past: http://genome.ucsc.edu/blog/the-new-ncbi-refseq-tracks-and-you/

For example, here is a session with these selections and the name2 field checked as well where the steps are Tools>Table Browser> Genes and Gene Predictions NCBI RefSeq Genes> table: UCSC RefSeq (refGene), region: position, output format: selected fields> get output

http://genome.ucsc.edu/cgi-bin/hgTables?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg19_RefSeqUCSC

Thanks, and again sorry for any confusion this may have caused!

Brian Lee
UCSC Genomics Institute

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