reconstructing operons from RNASeq


looking at the current publications there seem to be quite a bit of work on identifying SL1/SL2 sites from RNASeq libraries to identify operons. But I was wondering if anyone actually tried to reconstruct the polycistronic pre-mRNA from RNASeq.
I could find some comments on that they “contaminate” RNASeq assembly, and from personal experience it tends to throw off Cufflinks (which will then create some polycistronic mRNAs), but I couldn’t find any in-depth publication on it.

So I am wondering if the WormBase hive-mind has any insights on that.

thanks in advance