Hello,
A Table browser "save as sequence" result, using the "3' exons only" option,
based on the UCSC Genes track, should provide a fasta sequence for every
transcript in the primary table (all isoforms of the gene). Is this the result
that does not meet your needs? Genomic is not included - only the 3' UTR
("spliced" version, meaning = no introns) if that is what you specify in the
output options form.
If you have an example that follows this query path that does not meet your
needs, please email it to me and explain what you want to be different and we
can work together to figure out if there is another method that will give the
proper result.
Thanks,
Jennifer
------------------------------------------------
Jennifer Jackson
UCSC Genome Bioinformatics Group
> reposted on behalf of ----- "Gerome Breen" <[email protected]>
>
> >
> > Hi,
> > A query: We want to obtain a file with all 3'utr sequences as they
> > are in the different isoforms/splicoforms that make up the UCSC
> Genes
> > table. I have constructed a long and detail Galaxy workflow to do
> this
> > but it fails where different genes have overlapping UTR exons.
> >
> > I can see how to download UTR exons but what I need is the processed
>
> > UTR that is in each isoform in the UCSC gene table for every gene.
> >
> > Any help much appreciated.
> >
> > Best
> >
> > Gerome
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
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https://lists.soe.ucsc.edu/mailman/listinfo/genome
