Hi - Your question is not entirely clear on whether you need to identify gene fusion events from RNA-seq data. If this is what you are looking for, there are a list of tools that you can use to achieve this. Basically the goal is to find transcript reads that overlap or bridge two genes. Below is a recent benchmarking study using these tools, from which you can pick something that meets your needs. Best!

Article Accuracy assessment of fusion transcript detection via read-...

try this tool

https://github.com/nghiavtr/FuSeq

Check out this thread on the subject of detecting gene fusions in RNA-seq:

https://www.biostars.org/p/45986/