Hello, You are correct - a step was skipped to get the sequence, but since you just want a BED file anyway, do query #1. To get to #2, extra steps are needed, in particular if you want 3' mRna and not just genomic.
query#1 1) Table browser, UCSC Genes track 2) Filter as desired 3) Ouput = BED, give the output a name and download 4) Now select the 3' region. File exported will be a BED files with only the 3' regions query#2 1) In step #3 in query#1 above, save output as a custom track. Or, load up your BED output file as a custom track. 2) Table browser -> Custom track w/ 3' coordinates 3) Output as sequence. This will be the genomic sequence that corresponds to the cooridnates in the BED file (not the mRna from the orginal UCSC Gene's transcript). If you really need the mRna, then output the mRNa sequence in entirety and extract the 3' region using the knownGene's table using your own tools or check in the /kent utilities for help: http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities (faFrag, perhaps wrapped in a simple shell program would work if you have scripting resource). Does this help? Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Gerome Breen" <[email protected]> wrote: > From: "Gerome Breen" <[email protected]> > To: "Jennifer Jackson" <[email protected]> > Cc: "genome" <[email protected]> > Sent: Saturday, October 17, 2009 6:12:50 AM GMT -08:00 US/Canada Pacific > Subject: RE: [Genome] help > > 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
