Hi, The gtf file generated from hgTables has this error in the end:
chr10 rn4_refGene stop_codon 4326279 4326281 0.000000 + . gene_id "NM_001008876"; transcript_id "NM_001008876"; chr10 rn4_refGene exon 4326108 4326284 0.000000 + . gene_id "NM_001008876"; transcript_id "NM_001008876"; chr10 rn4_refGene start_codon 4293086 4293088 0.000000 + . gene_id "NM_001008876"; transcript_id "NM_001008876_dup1"; --------------------------------------------------------------------------- offsetToGenomic: need previous exon, but given index of 0 --------------------------------------------------------------------------- It is missing many chrs. The error existed on download made on Mar 17 and still exists today. Both view file in browser or gzip downloaded files have the same issue. The settings were: Mammal | Rat |Baylor3.4/rn4 Genes and Gene Prediction | RefSeq Genes refGene| * genome GTF - gene transfer format Hao Chen UTHSC _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
