I found the email below on the UCSC mailing list. I would also like a copy of extractGenes.pl if that is possible (I am also trying to movie to a new version of the UCSC type of tables of the flybase annotation). I couldn't find it in the UCSC source distribution. Let me know if you anticipate any problems with this.
More generally, I would like to get an updated version of the x flyBaseGene (in genePred format) and flyBaseNoncoding tables. I think I also need to use ldHgGene to do this? Thanks, Pouya (I sent a message about this to Angie already, but I realized I probably should have sent it here). ===================================================================== Angie Hinrichs angie at soe.ucsc.edu Tue Feb 23 10:51:15 PST 2010 Hi David, We don't have the resources to keep up with FlyBase updates. When we update our FlyBase Genes track, we also have to update many other related tables for the Gene Sorter and gene details, so it's more work than a simple track update. And we've got our plates full keeping up with our primary focus, vertebrate genomes. That said, you can find the instructions for updating flyBaseGenes in kent/src/hg/makeDb/doc/dm3.txt -- search for "FLYBASE 5.12 ANNOTATIONS". That section refers to a perl script, extractGenes.pl, that distills FlyBase's GFF3 into our local representation. That script is attached. If FlyBase haven't changed their GFF3 keywords since 5.12, it should still work. Hope that helps, Angie ----- "David Hoover" <hooverdm at helix.nih.gov> wrote: > From: "David Hoover" <hooverdm at helix.nih.gov> > To: genome-mirror at soe.ucsc.edu > Sent: Tuesday, February 23, 2010 7:02:39 AM GMT -08:00 US/Canada Pacific > Subject: [Genome-mirror] FlyBase tools > > I've noticed that the builds for the various Drosophila genomes are not > kept up with the releases from FlyBase. Why is that? > > Are there tools available in the jksrc tree for creating tables from the > FlyBase GFF files? It seems fairly straightforward... > > David Hoover > Helix Systems Staff > http://helix.nih.gov > _______________________________________________ > Genome-mirror mailing list > Genome-mirror at lists.soe.ucsc.edu > https://lists.soe.ucsc.edu/mailman/listinfo/genome-mirror _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
