Hello Rami,

The UCSC genome browser will result in one promoter sequence per transcript, as many genes will have many associated transcripts.


Depending on which track you are obtaining data from, a "representative" transcript for each gene may or may not be notated. If using "UCSC Genes", the tables associated with the primary table knownGenes to examine are knownIsoforms and knownCanonical, which will show how transcripts are clustered. You can link these tables together using the output option "selected fields from primary and related tables".

Alternatively, you may already have already selected a set of transcripts (not genes) to obtain data from. In that case, enter the identifiers directly into the UCSC Table browser's "identifiers" field when performing the query (paste or upload text file). Or pull all into Galaxy and join with your identifier list to subset the results. Identifiers must be in the same format as used by the track of interest for this method to work.

If you are having trouble with the Table browser, the UCSC Genome team can help through their mailing list at http://genome.ucsc.edu

Hopefully this helps to explain the data,

Best,

Jen
Galaxy team

On 7/25/11 10:25 AM, Rami Al-Ouran wrote:
Hello,

Is there a way in galaxy to retrieve the promoter sequences for a list
of genes. I tried using UCSC genome browser, but in many cases it keeps
giving more than one promoter sequence per gene.

Thank you,
Rami
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