What tools are best for conjoined gene/readthough detection and how do they differ from fusion gene detection?

Question

[Jeremy Leipzig]

What are the programs you would use to detect evens where (presumably adjacent) genes are spliced together but there are no genomic structural changes?

Seems like most gene fusion detection programs are also designed for RNA-Seq. How are these designed differently?

[WouterDeCoster]

JAFFA detects such events, but by default filters those from the results as the goal presumably is to identify actual genomic changes.