I performed an RNA-Seq experiment with a very heterogenous tumor sample. In this sample, I found a fusion gene transcript ( genes on different chromosomes), and also the WT gene transcripts. How can I check the quantification of this "fusion isoform" compared to the WT transcript ( see figure for more explanation ). I think using a count-based approach like DEXSeq. I don't know how other isoform quantification approach (RSEM, cufflinks,...) support fusion isoform (so isoform on different chromosomes). In final I just want to know the proportion of WT transcript 1, WT transcript 2 and the fusion transcript, and maybe compute a ratio.
What do you think ?