Historical versions of refGene files

[Soens, Zachry]

Dear UCSC,

 

I am trying to find copies of past versions of specifically the refGene table file (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz) and the corresponding gbCdnaInfo file that has transcript version information (http://hgdownload.cse.ucsc.edu/goldenPath/hgFixed/database/gbCdnaInfo.txt.gz) because I need to determine the genomic positions of variants referred to by HGVS expressions with old transcript versions (NM_123.old):c.8A>C).  Can you advise if such files are present in an archive somewhere or if there is a better way of going about this?

 

Thank you,

 

Zach Soens, PhD

[Brian Lee]

Dear Zach,

Thank you for using the UCSC Genome Browser and your question about obtaining older versions of the refGene table.

When you write NM_123.old, does that relate to some kind of equation where old equals some past accession version number?

We might be able to help you acquire this information from NCBI and we might have some older data available. Can you reply off list to me or to our private genom...@soe.ucsc.edu internal list with some id's you are looking for?

Also another engineer suggests if you are looking to do HGVS transcript to genomic positions, VariantValidator.org and/or mutalyzer.nl might be useful. VariantValidator.org uses the Universal Transcript Archive, so that it might support most older versions of RefSeq transcripts.

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

UC Santa Cruz Genomics Institute

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