Hello, Miriam,
It sounds like maybe you are getting the splice isoforms and therefore
more than one "gene" per probe. When using the Table Browser, you
should use the knownCanonical table, which has only one isoform
per gene. There is not a good way to upload more than 1000 at
a time unless you make a custom track of your data, but then the
intersection with the knownCanonical table may cause you to lose
the names of either your probe or the gene.
We are working on a way to preserve more information from both
tables during an intersection, but in the meantime, are referring
people to the excellent tools at the Galaxy site (you can export
output directly to Galaxy from the Table Browser).
I hope this response is enough to get you going in the right direction.
If you require more detailed information or get stuck at a different
point in your process, please do contact the mailing list again.
You should know that we are updating the UCSC Genes track and the
dozens of tables that intersect with it. We hope to have the new
version out fairly soon. You can watch the main page (or the
genome-announce low-volume mailing list) for news about the release.
good luck in your work and best wishes,
--b0b kuhn
ucsc genome bioinformatics group
On 1/20/2012 9:03 AM, Miriam Ragle Aure wrote:
> Hi!
>
>
>
> I am trying to convert genomic positions from a microarray annotation
> file into gene names with hope of getting the "newest", most updated
> gene name. I have tried using the table browser in UCSC, but the problem
> is that when I upload a list of coordinates, the resulting list with
> gene names is not the same size (some positions give me more than one
> gene name and some doesn't give any at all). Thus, I am not able to map
> the list of genomic positions to the output list with gene names because
> the rows are not matching. Is it possible to get an output file matching
> the input and output? (Also, you are only allowed to upload 1000 rows
> at a time, but is it somehow possible to circumvent this, uploading,
> say, 26k rows?)
>
>
>
> Thanks a million!
>
>
>
> Best regards,
>
>
>
> Miriam
>
>
>
> _______________________________________________
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