Apparently my issue is nicely squared by gff3ToGenePred in http://hgdownload.cse.ucsc.edu/admin/exe
Sorry for the noise. On Tue, Nov 15, 2011 at 7:05 PM, Jacob Biesinger <[email protected]>wrote: > Hi! > > A post last year asked about converting from gff3 files to the UCSC gene > table format (quoted below). I find myself needing to do the exact sma > ething but for Xenopus Tropicalis build 7.1 (xenTro4? ANy idea when this > build will be available?). All the scripts I've written work around the > UCSC format (my mistake, I guess) and it would be nice to be able to work > on genomes that are unhosted by UCSC. > > Could a little more information be given on how you guys are doing this? > (a script would be ideal). > > Thanks for the tools. > > > > <quote> > > Good Afternoon Julie: > > This appears that you are looking at this gene on C. elegans. > I have already converted the WormBase gff3 gene prediction files > to genePred tracks in the newest C. elegans browser now under > development. You can see these genes in the "WormBase Gene" tracks > at:http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?db=ce9&position=chrI:4119-10232 > > Please note, this is our test browser and the information is subject > to change. > > Note, there are extra tracks for RNAs and PseudoGenes from the WormBase > gff3 file. > > It is quite an involved procedure to scan the WormBase gff3 files to > get out the required information to make gene tracks from that. > Fields 2, 3 and 9 of the gff3 file need to be scanned and converted > to work with our conversion tools. > > --Hiram > > ----- Original Message ----- > From: "Julie Ahringer" <ja219 at cam.ac.uk > <https://lists.soe.ucsc.edu/mailman/listinfo/genome>> > To: genome at soe.ucsc.edu > <https://lists.soe.ucsc.edu/mailman/listinfo/genome> > Sent: Wednesday, October 13, 2010 3:52:33 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] gff3 to UCSC gene table? > > Do you know how I can convert a gff3 file of gene features to a UCSC > gene table like this: > > #name chrom strand txStart txEnd cdsStart cdsEnd > exonCount exonStarts exonEnds proteinID > Y74C9A.3.1 chrI - 4123 10232 4220 10148 5 > 4123,5194,6036,9726,10094, 4358,5296,6327,9846,10232, > Y74C9A.3 > > Thanks, > > Julie > -- > ___________________________________ > Dr. Julie Ahringer > The Gurdon Institute > University of Cambridge > Tennis Court Road > Cambridge CB2 1QN > UK > > phone +44 1223 334142 (Office) > 334144 (Lab) > fax +44 1223 334089 > NOTE NEW EMAIL ADDRESS: ja219 at cam.ac.uk > <https://lists.soe.ucsc.edu/mailman/listinfo/genome>http://www.gurdon.cam.ac.uk/~ahringerlab/ > > </quote> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
