Dec 2009 track

[Gemma Hyland]

Hi,

I am currently carrying out a research project and using TCGA exon quantification data but I'm having trouble mapping the co-ordinates to transript ID's. According to their website they used the reference transcript set on the hg19 UCSC Gene standard track(December 2009 version). I was wondering if that were still available as I can't find it on the website. Would it be possible to get this file or could you could you tell me where to find it?

Kinda regards,

Gemma

[Matthew Speir]

Hi Gemma,

Thank you for your question about obtaining the UCSC Genes build from 2009.

You can obtain this from the Table Browser using the following settings:

1. Navigate to the Table Browser, https://genome.ucsc.edu/cgi-bin/hgTables.
2. Make the following selections:
    clade: Mammal
    genome: Human
    assembly: Feb. 2009 (GRCh37/hg19)
    group: All Tables
    database: hg19
    table: knownGeneOld5
    output format: BED - browser extensible data
    output file: enter a file name or leave blank to view results in the browser

3. Click "get output".

You should now have a BED file, https://genome.ucsc.edu/FAQ/FAQformat.html#format1, that contains all of the UCSC Genes predictions for that release. Or you can download the table in genePred format, https://genome.ucsc.edu/FAQ/FAQformat.html#format9, from our downloads server here: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownGeneOld5.txt.gz.

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

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