I recently ran FusionCatcher with default params/default Ensembl v98 build on two separate paired-end tumor RNA samples. The first resulted in ~40 fusions called, while the second resulted in ~3000 fusions called (where only a small % total are labeled by FusionCatcher as being likely false positives).
I'm assuming that it's unlikely that there are this many fusions in the second sample, although my understanding is that FusionCatcher attempts to filter enough so as to avoid situations like this with thousands of false positives. Are there any obvious issues in RNA samples/prep/sequencing/etc. that might result in so many fusions being called?
(Interestingly, when I run this same sample with STAR-Fusion, I get 0 fusions that meet STAR-Fusion's minimum FFPM threshold.)
