Wrong exon number information from tophat-fusion

[angerusso]

I posted this question in "BioInformatics" as well to someone who experienced similar problem with no answers. Any solutions from the RNASequencing forum?

It appears to me that somehow tophat doesn't take into account the strand information? Please help!

I also experienced similar problem with well known fusion.

Expected fusion in my sample is TMPRSS2(Exon1) with ERG. What I obtain is TMPRSS2 (exon14) with ERG which doesn't make sense.

Is there a solution to this problem? Please suggest how to get the right fusions from tophat-fusion?

Thanks so much~!