Even more concisely, if you have your $HOME/.hg.conf file setup: $ genePredToGtf mm9 ensGene ensGene.gtf
to allow genePredToGtf to read the ensGene table directly from the public MySQL server. Hiram Clawson wrote: > If you have the kent utility genePredToGtf, you can convert the UCSC genePred > format file directly into the gtf format: > > $ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N \ > -e "select * from ensGene;" mm9 | cut -f2- | genePredToGtf file stdin > ensGene.gtf > > The linux x86_64 version of this binary can be found here: > > http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ > > --Hiram _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
