Hello Scott, The "refGene" table has essentially the same data (plus a few extra data columns). Basically, use refGene.name2 and place that at the start of the refGene file and leave off the last few columns and the data would be the same.
If any data you are looking at does not have a refGene.name2 column, then the gene name is not available from RefSeq. Hopefully this helps, please feel free to contact the mailing list support team again if you would like more assistance. Regards, Jen UCSC Genome Browser Support On 7/26/10 5:19 PM, Scott Alexander Lindsay wrote: > Hi, > > I am looking for RefFlat files for a couple of genomes that I am > working with, but I think they are absent. For example, Drosophila > virilis has refLink, refSeqStatus and refSeqSummary files but no > refFlat. This is the same for other genomes I am looking at as well. > Is there any way I can somehow generate these files? Or use something > similar? I basically just need a file in RefFlat format so that a > program can generate an exon coordinates set and splice junction > set. I noticed that xenoRefFlat exists for a number of them, but I > have been reading the mail archives and I don't think this is what I > want. > > I also wondered why the annotation database folder was absent for the > more recent release of the D virilis genome. This is the same again > for other genomes I am working with. They were released a number of > years ago. > > Thanks for your help. > > Scott > > ================================== > Scott Lindsay, PhD > Section of Cell and Developmental Biology > Division of Biological Sciences > Bonner Hall, Room 4401 > University of California, San Diego > La Jolla CA 92093-0349 > (858) 822-2409 > ================================== > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
