High 5' expression
If the 5' read count is very high compared to the EXPR_CONTROL read count, the 3'/5' Imbalance value is not a reliable predictor. With high 5' read counts, the potential for false negatives (missing a real fusion) increases.
The plot linked here shows a false negative in sample 32. The green line tracks the 5' expression as 5' read counts divided by EXPR_CONTROL read counts. Note the spike of high 5' expression at the false negative for sample 21.
We have not seen a high 5' expression to be associated with a false positive.