Hello Moritz, Here is our FAQ on the GTF format: http://genome.ucsc.edu/FAQ/FAQformat#format4
----- "Moritz Gilsdorf" <[email protected]> wrote: > Hi, > > I think there¹s a problem with generating a GTF from the refGene > Table. The > output of the Table Browser looks like this: > > chr21 hg19_refGene start_codon 33032083 33032085 0.000000 + . gene_id > "NM_000454"; transcript_id "NM_000454"; > chr21 hg19_refGene CDS 33032083 33032154 0.000000 + 0 gene_id > "NM_000454"; > transcript_id "NM_000454"; > chr21 hg19_refGene exon 33031935 33032154 0.000000 + . gene_id > "NM_000454"; > transcript_id "NM_000454"; > chr21 hg19_refGene CDS 33036103 33036199 0.000000 + 0 gene_id > "NM_000454"; > transcript_id "NM_000454"; > chr21 hg19_refGene exon 33036103 33036199 0.000000 + . gene_id > "NM_000454"; > transcript_id "NM_000454"; > chr21 hg19_refGene CDS 33038762 33038831 0.000000 + 2 gene_id > "NM_000454"; > transcript_id "NM_000454"; > chr21 hg19_refGene exon 33038762 33038831 0.000000 + . gene_id > "NM_000454"; > transcript_id "NM_000454"; > > I think the values after gene_id should be the gene names instead of > the > transcript id¹s. Please correct me if I¹m mistaken. > > Best, Moritz > > > -- > Moritz Gilsdorf > Boutros Group (Signaling and Functional Genomics) > GoBio Project > DKFZ Heidelberg > Phone +49 6221 421958 > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
