tophat-fusion-post multiple transcript fusions in a single hit?

Question

[benformatics]

Hello everyone,

I just finished pushing some fruit fly data through TopHat-Fusion and the post filtering part. I was noticing some peculiar things in the final results.html output files that were produced. For the most part everything looked good but in some cases individual result tables showed multiple genes:

1. chrX-chrX ff

nsonlytheo         CG2930     chrX     3767208     ec          chrX     3714758     3      0     0
nsonlytheo         CG2930     chrX     3767208     ec          chrX     3714758     5      0     0
nsonlytheo         CG2930     chrX     3767208     ec          chrX     3745969     11     0     0
nsonlytheo         CG2930     chrX     3767208     ec          chrX     3745969     4      0     0
nsonlytheo         CG2930     chrX     3767208     ec          chrX     3745969     6      0     0
nsonlytheo         CG2930     chrX     3767208     ec          chrX     3745969     9      0     0
mutantonlytheo     CG2930     chrX     3767208     ec          chrX     3745969     4      0     0
mutantonlytheo     CG2930     chrX     3767208     ec          chrX     3745969     10     0     0
mutantonlytheo     CG2930     chrX     3767208     ec          chrX     3745969     9      0     0
mutantonlytheo     CG2930     chrX     3767208     ec          chrX     3745969     4      0     0
mutantonlytheo     CG2930     chrX     3767208     ec          chrX     3745969     7      0     0
mutantonlytheo     CG2930     chrX     3767208     ec          chrX     3745969     8      0     0
mutantonlytheo     CG2930     chrX     3767208     ec          chrX     3745969     12     0     0
nsonlytheo         tyf        chrX     4014456     CG43689     chrX     3978842     3      0     0
mutantonlytheo     tyf        chrX     4014456     CG43689     chrX     3979650     3      0     0
mutantonlytheo     tyf        chrX     4014456     CG43689     chrX     3979650     4      0     0
mutantonlytheo     tyf        chrX     4014456     CG43689     chrX     3978842     3      0     0

Any reason why I might expect to see something like this? The only obvious things are that both fusions are "ff" and between the same two chromosomes?

Anybody else run into this?