Hello Cheng, You can use the Table Browser to create a RefSeq Genes track output in GTF format (GTF has a slightly more structured 9th data field, but is otherwise identical to GFF format).
File type help (scroll down to see both GFF & GTF format definitions): http://genome.ucsc.edu/FAQ/FAQformat.html#format3 Table browser help: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Query path: 1) open Table browser http://genome.ucsc.edu/cgi-bin/hgTables and navigate to your genome & the RefSeq Genes track 2) select output = GTF, name the file for download, submit and choose your options. It is important to note that the GTF file will not have the Gene name in the output; the transcript name is used for both data values labeled as gene_id & transcript_id. To get the Gene name, start the query over with the same track, but set: 3) output format to be "selected fields from primary and related tables", name the file, and submit. On the next page, select the name & name2 data fields and get data. 4) Using your own tools, substitute the gene2 field (Gene name) into the GTF file "gene_id" value, based on the name field (Transcript name). I hope this information is helpful. Please feel free to contact the help mailing list again if you require further assistance. Best regards, Jen UCSC Genome Browser Support http://genome.ucsc.edu/contacts.html [email protected] [email protected] On 7/12/10 1:24 AM, 程艳兵 wrote: > Hi, > my work needs a gene structure annotation file in gff file to indicate > the position of exon, intron, UTR, CDS of each refseq mRNA in human > genome hg18. I can't find such annotation file in UCSC FTP. So i'm > wondering whether this annotation file exist in UCSC FTP. > > Best regards, > > Cheng > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
