Evaluation of false negative and false positive rates of SOAPfuse based on simulated datasets. A comparison among three tools based on simulated fusion events is shown with different expression levels of the fusion transcripts. (a,b) FN rate (a) and FP rate (b) of three tools are shown in line graphs. (c) Distribution of 142 simulated fusion events detected by the three methods. SOAPfuse missed three simulated fusion events (red) that were identified by both deFuse and TopHat-Fusion.