Supporting and contradicting evidence for fusion transcripts. (a) Given a fusion point and the chromosomes (gray) spanning it, single-end and paired-end reads (blue) support the fusion. Other reads (red) contradict the fusion by mapping entirely to either of the two chromosomes. (b) TopHat-Fusion prefers reads that uniformly cover a 600-bp window centered in any fusion point. On the upper left, blue reads cover the entire window. On the lower left, red reads cover only a narrow window around the fusion. On the lower right, reads do not cover part of the 600-bp window. The cases shown in orange will be rejected by TopHat-Fusion.