Hi Li, Please see this section of our help describing the GTF file format: http://genome.ucsc.edu/FAQ/FAQformat.html#format4.
If you want generate the data exactly like the table schema, for the output format in the Table Browser, select "All fields from selected table". Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 7/11/11 1:13 PM, Jia, Li (NIH/NCI) [C] wrote: > Hi, > > I am using table browser working on generating annotation GTF format. After > selecting assembly of interest select: > > group: Genes and Gene Prediction Tracks > track: refSeq Gene > table: refFlat > output format: "GTF"--Gene transfer format > > then give the name and output the GTF file. > > My question is that my output refFlat.GTF is not exactly same as the > described table schema. In table schema, output format is as follows: > > geneName LOC100288778 > Name NR_028269 > chrom chr1 > strand - > txStart 4224 > txEnd 7502 > cdsStart 7502 > cdsEnd 7502 > exonCount 7 > exonStarts 4224,4832,5658,6469,6719,70... > exonEnds 4692,4901,5810,6631,6918,72... > > but my output file is: > chr1 hg18_refFlat exon 14601 14754 0.000000 - . > gene_id "WASH7P"; transcript_id "WASH7P"; > chr1 hg18_refFlat exon 19184 19233 0.000000 - . > gene_id "WASH7P"; transcript_id "WASH7P"; > chr1 hg18_refFlat exon 24474 25037 0.000000 - . > gene_id "FAM138A"; transcript_id "FAM138A"; > chr1 hg18_refFlat exon 25140 25344 0.000000 - . > gene_id "FAM138A"; transcript_id "FAM138A"; > > it has GeneName (gene_id), but there is no trancript_id (in the output, it is > same as gene_id). In the example schema, Name should be transcript_id? > > How do I generate the table exactly like the table schema? > > Thanks, > Li > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
