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
