Hi John, Another Kent source utility to try is ldHgGene, which translates GFF version 1 or GTF into the genePred format. That is the program that we use to load GFF/GTF files into our database. When we get a GFF3 file, we write a little sed or perl script to translate it into one of our recognized flavors of GFF/GTF, and then use ldHgGene. You will want to use the -out=file.gp option so that it creates a file instead of trying to load a mysql database table.
Hope that helps, Angie ----- "Jennifer Jackson" <[email protected]> wrote: > From: "Jennifer Jackson" <[email protected]> > To: "John Malone" <[email protected]> > Cc: [email protected] > Sent: Friday, November 6, 2009 9:31:25 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] convert GFF3 to refFlat.txt (genePred) > > Hello, > > We do not have a utility to do that particular conversion, but we do > have the reverse for an earlier version of the GTF format. Perhaps it > would be a place to start when creating your own? It is is the kent > source tree: > > gpToGtf > http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities > > One option may be to try to load the data as a custom track, then > output the data in genePred format using the Table browser. There are > a few versions of GFF/GTF format and not all sources are consistent > with the formatting rules. These are the description we use: > http://genome.ucsc.edu/FAQ/FAQformat#format3 > http://genome.ucsc.edu/FAQ/FAQformat#format4 > > Also, these prior mailing list answers may be helpful: > Open google and paste in "gtf > site:lists.soe.ucsc.edu/pipermail/genome" > > We hope this is helpful. I am not sure how familiar you are with the > browser, but just in case, more details for the Table browser, Custom > Tracks, etc. can be found by using the top blue navigation bar links > Help & FAQ, but if you would like specific pointers or have a > question, please ask. > Jennifer > > ------------------------------------------------ > Jennifer Jackson > UCSC Genome Bioinformatics Group > > ----- "John Malone" <[email protected]> wrote: > > > From: "John Malone" <[email protected]> > > To: [email protected] > > Sent: Friday, November 6, 2009 3:43:21 PM GMT -08:00 US/Canada > Pacific > > Subject: [Genome] convert GFF3 to refFlat.txt (genePred) > > > > Hi, > > > > I'd like to convert a GFF3 file into a refFlat (genePred) file. Do > > > you have a script that will do this? > > > > Thanks, > > > > John > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
