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Old 11-19-2012, 08:34 PM   #22
Location: USA

Join Date: Nov 2012
Posts: 11

I tried to run cufflinks after TopHat mapping and as a genome reference annotation it requires a file in gtf format. I downloaded the genome annotation from the JGI website (I am working with a fungus whose genome was sequenced in 2010). The file annotation that I have is in gtf, but when I extract it it becomes gff, a format not supported by cufflinks in Galaxy. I converted my file with the workflow found at The generated genome annotation is in the gtf format (the only difference that I see is in the first column, scaffold become chrscaffold), but when I run cufflinks all the output were 0. Now I am running again cufflinks without using the annotated genome to see if there is any difference in the results. I was wondering if the conversion that I did is correct, if anyone knows if there is another way to do it, or if I should email JGI people to see if they have a GTF format for the genome annotation I need. I don't think I can go ahead with the analysis without a genome annotation in GTF.
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