Recently, we performed paired end RNA-seq. and last week I got detected translocation list from our bioinformatician. In the file that I have there are both genes involved in the fusion transcript and also number of split and span reads and sequence of the fusion (almost 150 bp from each side). Now, I am trying to BLAT this sequences, make pictures for each fusion gene, design the primer and sequence them for validation. But, I have some problems with some of the fusions. In some of the cases I have complementary sequence of gene A fused with correct sequence of gene B (both genes in the same direction in the chromosome). How can this happen? Is it because of inversion (in the report, indicated that there is no inversion)? How should I design the primers; should I used reference genome for primer design or the sequence that I have from RNA-seq? Thank you very much.