Good Morning Irwin: We are looking into this problem. In the mean while, you can pick up our information for the Ensembl genes from our database files in UCSC genePred format: http://hgdownload.cse.ucsc.edu/goldenPath/xenTro2/database/ensGene.sql http://hgdownload.cse.ucsc.edu/goldenPath/xenTro2/database/ensGene.txt.gz http://hgdownload.cse.ucsc.edu/goldenPath/xenTro2/database/ensGtp.sql http://hgdownload.cse.ucsc.edu/goldenPath/xenTro2/database/ensGtp.txt.gz http://hgdownload.cse.ucsc.edu/goldenPath/xenTro2/database/ensPep.sql http://hgdownload.cse.ucsc.edu/goldenPath/xenTro2/database/ensGtp.txt.gz
If you want these in the GTF format, you can find them directly at Ensembl: ftp://ftp.ensembl.org/pub/release-59/gtf/xenopus_tropicalis/Xenopus_tropicalis.JGI4.1.59.gtf.gz --Hiram Irwin Jungreis wrote: > I am trying to get the gene annotations for X. tropicalis from here: > http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=170244280&clade=vertebrate&org=X.+tropicalis&db=xenTro2&hgta_group=genes&hgta_track=ensGene&hgta_table=0&hgta_regionType=genome&position=scaffold_27%3A565941-578374&hgta_outputType=gff&hgta_outFileName=xenTro2.JGI4.1.Aug2005.Ensembl.gtf.gz > > I've tried downloading several versions of the GTF file (Ensembl > Genes, RefSeq Genes, and TransMap mRNA) and in all cases the file > appears to be truncated and ends with the lines: > > --------------------------------------------------------------------------- > Allocated too much memory - more than 6,442,450,941 bytes > (6,442,678,139) > --------------------------------------------------------------------------- > > This happens whether I download plain text or gzip, so it isn't a > problem with the decompression. > > Does anyone know where I can get the complete GTF file, and if there > is someone else who should be notified about this? > > Thanks. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
