Hi Ken, The method suggested by Brooke earlier should work. Maybe the problem is how to get the data out of the Table browser? The original question was a bit confusing as it specifies "Known Genes" which is actually a reference to the "UCSC Genes" track, but the fasta data example in the question is actually from the "RefSeq Genes" track.
To simplify, consider just the "RefSeq Genes" track as the base. Send the data over to Galaxy as two distinct output files, then use the text manipulation tools in Galaxy to merge into one. 1) the NM_* -> Gene association 2) the fasta sequence with NM_* in the description line Was the problem with #1? To do this, extract refGene.name and refGene.name2 using output format "selected fields from primary and related tables". Do not use the default BED format, as this would not have the extra field refGene.name2 included. Join on refSeq.name (the transcript identifier) to link in refSeq.name2 (the gene symbol). To do #1 for the "UCSC Genes" track, the extract kgXref.kgID and kgXref.geneSymbol (and/or any of the other fields in this table). Other tables such as kgAlias could potentially also be used, but these can be one->many relationships, which add another layer of complexity to the join. If your problem was with some other Table browser function, would you be able to provide more detail? Thanks, Jen UCSC Genome Browser Support On 8/11/10 8:51 AM, Kenneth Bryan wrote: > Dear Genome Browser team, > > some time ago the list received a question: > > https://lists.soe.ucsc.edu/pipermail/genome/2008-March/thread.html#15822 > > regarding the manipulation of fasta headers in the sequence output option. > I was unable to achieve the suggested course via Galaxy > > Currently is there any way to achieve this? > > Thanks, > > Ken > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
