Hi I am afraid I only see options for genomic protein mRNA
when I tried this this morning. Selecting mRNA gives the fasta delimited mRNA sequences. What is happening? I basically would like a 3'UTR bed file/table in the same format as the knowngenes table and then I could use it for a lot of miRNA prediction work. Best Gerome ________________________________________ From: Jennifer Jackson [[email protected]] Sent: 16 October 2009 19:27 To: Breen, Gerome Cc: genome Subject: Re: [Genome] help 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
