hi Scott, Re: your question about the annotation database folder, this is present only if we provide a browser for the assembly. I believe we did not provide full browsers for several of the recent flies -- they are used only in the 15-insect conservation track on the dm3 D. melanogaster browser. Therefore, they have no annotations, and you see only the assembly and liftOver folders for these.
-Donna On 7/26/2010 6:18 PM, Jennifer Jackson wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
