Hello,
I've been working with tophat for a while pretty successfully, but for some reason this one data set will not cooperate. Using the .gff file I downloaded for the corresponding genome I get:

[Fri Jul 9 15:45:42 2010] Reading known junctions from GFF file
Warning: TopHat did not find any junctions in GFF file
I've tried making several adjustments to the file to make it fit the prescribed format. I've also double checked that the first column matches whats in the bowtie index using bowtie-inspect. Maybe someone else has had a similar experience? I've tried several variants on the following format and nothing helps, which makes me thing is probably something I've overlooked and I am out of ideas.

Chr01 glean gene 47206323 47208329 . - . ID=BGIOSGA000006;Name=BGIOSGA000006;
Chr01 glean mRNA 47206323 47208329 0.999993 - . ID=BGIOSGA000006;Name=BGIOSGA000006-TA;Parent=BGIOSGA000006;ID=BGIOSGA000006.50;Name=BGIOSGA000006-TA;ID=BGIOSGA000006;
Chr01 glean exon 47208026 47208329 . - 0 Parent=BGIOSGA000006;ID=BGIOSGA000006.51;
Chr01 glean exon 47207590 47207951 . - 2 Parent=BGIOSGA000006;ID=BGIOSGA000006.52;
Chr01 glean exon 47207158 47207394 . - 0 Parent=BGIOSGA000006;ID=BGIOSGA000006.53;
Chr01 glean exon 47206323 47206556 . - 0 Parent=BGIOSGA000006;ID=BGIOSGA000006.54;
Thanks in advance.