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Downloading genes annotations from UCSC Table Browser
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3.2 years ago
khorms • 30
Moscow

I want to download genes annotations from UCSC Table Browser. Although, all the tables I found there (including refSeq, GENCODE, UCSC Genes and some others) included information for mRNA transcripts but not for genes. It means, that for a single gene any of these tables contains several lines describing different transcript variants. I want a table containing a single line per every gene. Where can I find it? Thank you.

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Does that make sense? What should that line contain if that gene has multiple alternative transcripts?

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Every line should contain the coordinates of gene and its name. As far as I know, the cross-spliced transcripts (the transcripts made of exons from different genes) are not included in these annotation files, so all the transcript variants of the same gene should belong to the same genomic region. So if we take all the transcript variants of the same gene and merge their coordinates then we get the coordinates of gene. It can be made as a separate procedure but I'm sure it has been done already so I wonder where can I find this information. And of course yes, for some kind of analysis it makes sense because number of transcript variants can give additional bias.

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18 months ago
PoGibas 4.8k
Vilnius

Why to download GENCODE from UCSC, but not from https://www.gencodegenes.org directly? As far as I remember their annotations contains "gene" information too.

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That works, thank you!

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