Hi Kenny, Yes, the format for the primary table of the RefSeq Genes track is genePred. You can find this out by clicking on the "schema" link from the track description page or from the Table browser.
This is the FAQ for all files: http://genome-test.cse.ucsc.edu/FAQ/FAQformat And for genePred in particular: http://genome-test.cse.ucsc.edu/FAQ/FAQformat#format9 Jenn ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- [email protected] wrote: > From: [email protected] > To: "Jennifer Jackson" <[email protected]> > Cc: "kenny daily" <[email protected]>, [email protected] > Sent: Friday, October 23, 2009 7:22:47 PM GMT -08:00 US/Canada Pacific > Subject: Re: Re: [Genome] Columns missing in refGene (example, rn4) > > Is there somewhere that documents what columns are "required" for that > type? > > Thanks, > > Kenny > > On Oct 23, 2009 7:00pm, Jennifer Jackson <[email protected]> wrote: > > Hi Kenny, > > > > > The data was created by slightly different processes, however all > follow > > the general specification for the file type. The extra columns are > > > optional. Our best advice is to create a routine in the utility you > use > > to parse the data to either use or ignore the extra data if it is > there > > and to allow it to be absent. > > > > > We are making the assumption that you do not need the data in the > extra, > > optional columns (since a NULL would be OK). If we have this wrong, > > > please correct us. > > > > > Jennifer > > > > > > > ------------------------------------------------ > > > Jennifer Jackson > > > UCSC Genome Bioinformatics Group > > > > > ----- "kenny daily" [email protected]> wrote: > > > > > > From: "kenny daily" [email protected]> > > > > To: [email protected] > > > > Sent: Thursday, October 22, 2009 12:04:54 PM GMT -08:00 US/Canada > > > Pacific > > > > Subject: [Genome] Columns missing in refGene (example, rn4) > > > > > > > > Why are there different columns for refGene tables, depending on > the > > > > species? For example, rn4 is missing name2, cdsStartStat, > cdsEndStat, > > > > and > > > > exonFrames. If this data does not exist, is it possible for you to > add > > > > these > > > > columns with NULL data? It's cumbersome to change reading > functions > > > > for > > > > different species when wanting to use this data and the columns > > > > available > > > > are not predictable. Thank you. > > > > > > > > -- > > > > Kenny Daily > > > > [email protected] > > > > http://www.kennydaily.net/ > > > > > > > > --- Prediction is very difficult, especially about the future. > (Niels > > > > Bohr) > > > > --- > > > > _______________________________________________ > > > > Genome maillist - [email protected] > > > > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
