I am looking for tools specifically designed for the identification of trans-splicing events given a bulk RNA dataset from long read data (specifically, I have nanopore cDNA libraries).
I found the tool JAFFAL, as well as many tools designed for Illumina PE libraries such as STAR-SEQR and SLIDR-SLOPPR that could probably be tuned to accept full transcripts. However, all the available tools I've found seem to only be able to identify events of spliced leader trans-splicing, and cannot identify any of the other mechanisms.
Specifically, one of the known trans-spliced genes in my model is the Bursicon gene, where exon 3 is on a different chromosome arm to exons 1, 2, and 4. It would be great to use this as a positive control in appropriate datasets. I would also be interested in tools that can identify sense anti-sense splicing if they exist.
