rat gtf question

[Christa-Lynn Blenck]

Hello,

I recently used your genePredToGtf program for the rat rn6 genome to create a gtf file in which the gene ID and transcript ID were different. I was able to get this to work and have been using the output gtf for my subsequent analysis. When I was taking a closer look at my gtf file today I noticed something this looks a little strange. At the end of each gene after the last exon or CDS is listed, I then get the coordinates/info for the stop/start codon, and while the coordinates appear to be correct, the exon number that is referenced in both the start and stop codon is always (or from what I have seen) listed as exon number 1, but shouldn’t it be in an exon after number 1? I have attached an example in which it looks like the stop codon should be in exon 2, not exon 1. Is this just a bug in the genePredToGtf program? Will it affect my analysis?

Thanks for the help,

Christa Blenck

[Steve Heitner]

Hello, Christa.

This is indeed a bug in genePredToGtf. Thank you for reporting this to us. It is too late to get a fix into our current software release which is scheduled to go out this upcoming Tuesday April 28. The fix should be available with our next release which is scheduled for Tuesday May 19.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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