As we know that fusion transcripts could be a result of genomic translocation events, or could be due to trans/cis splicing events among mRNA. Let's naively call them gene fusions and transcript fusions. Now there are a ton of tools that predict transcript fusions from RNA-seq data. Can these tools distinguish between these two types?
Like for a given fusion predicted, can they say whether it must have been due to genomic rearrangements or fusion at the mRNA level? Or is this not even possible?