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
