Hi Nienke, I was wondering if we could get a little more information about the update you are referring to and which assembly and region you are using (if you prefer, you can provide the region off-list to at [email protected]) . Also, I think it would be helpful if you could provide the dates on which you obtained the initial set of data and the second set of data form our site.
Regarding the update, are you referring to the daily Genbank update that occur nightly (more information here: http://genome.ucsc.edu/FAQ/FAQreleases#release6), and which updates the RefSeq Genes track "Data Last updated" stamp each time it runs? For example, today on the page linked to below it states, "Data last updated: 2010-01-07". http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=refGene Also, we recently (mid-December) we switched the default human assembly from hg18 to GRCh37 (hg19), and if your results from before the update were on hg18 and your results from after the update are on GRCh37, then, because of the coordinate changes from hg18 to GRCh37, the same coordinate range might actually be covering two different regions in the two different assemblies. I look forward to receiving this information so that I can help answer your questions. Thank you, Katrina Learned UCSC Genome Bioinformatics Group [email protected] wrote: > Dear sir/madam, > > > > In our department we have a tool to generate a Nimblegen array design, > based on the tables with RefSeq and UCSC gene information ("refGene" and > "knownGene"). A collegue was comparing results we got before the update > with results we got after the update, and we saw a big difference in > number of coding bases in a specific location on the genome. > > > > In total we have a region of 12.2Mb and in here we saw an increase of > +/- 23 kb. > > > > We are wondering what you changed in the refGene table with this new > update. Are there new genes available, or is it information about the > exons (new exons in genes)? Or maybe something else/more? > > > > I am looking forward to your reply. > > > > Kind regards, > > Nienke Wieskamp > > > > > > > Het UMC St Radboud staat geregistreerd bij de Kamer van Koophandel in het > handelsregister onder nummer 41055629. > The Radboud University Nijmegen Medical Centre is listed in the Commercial > Register of the Chamber of Commerce under file number 41055629. > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
