Hello Hao Chen, Thank you for including the Table Browser settings you used when you saw the error. You have uncovered a bug in our Table Browser GTF output format. We have corrected the error, but the fix will not be on our public site until next week. In the meantime, you can download this data using our test site, http://genome-test.cse.ucsc.edu. Note that in general that site contains a lot of experimental and untested data.
Thank you for bringing the error to our attention. Please let us know if you encounter any further problems. -- Brooke Rhead UCSC Genome Bioinformatics Group Hao Chen wrote on 3/27/11 12:56 PM: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
