TophatFusion_Antation_Amplification

[Charitra]

can somebody tell me tophat_fusion annotation alignment ?
I have aligned my RNA-seq with refhg19 which is not RNA-seq.
while getting fusion, I have to get fusion location and design primer... and get the fusion protein amplified.

is it the standard methodology mapping reads with hg19 (annotation)?
if it is not the case and have to map agains ref hgRNA-seq then transcriptome is time/condition specific and how other methodology can predict best fusion ?
anybody have idea ?

expecting kind replies.

Thanks