Good Afternoon Hao Chen:
If you have the kent utility: genePredToGtf, available from:
http://hgdownload.cse.ucsc.edu/admin/exe/
You can fetch this data directly from the public MySQL server:
$ mysql -N --user=genome --host=genome-mysql.cse.ucsc.edu -A \
-e "select * from refGene;" rn4 | cut -f2- \
| genePredToGtf file stdin rn4.refGene.gtf
--Hiram
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
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