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Table 2 A comparison of fusion detection performance on simulated RNA-Seq, 250 bp simulation of 120 fusions

From: JAFFA: High sensitivity transcriptome-focused fusion gene detection

Tool True positives False positives
Total Fusion gene coverage
100× 50× 10×
JAFFA 86 (71/14/1) 20 19 17 18 8 4 3 (1/1/1)
SOAPfuse 61 16 17 14 11 1 2 79
deFuse 58 20 15 13 10 0 0 118
FusionCatcher 56 18 16 11 9 1 1 78
TopHat-Fusion 22 11 10 1 0 0 0 0
  1. JAFFA and alternative tools were run on a MiSeq simulation of 120 fusions: 20 fusions at each of 1×, 2×, 5×, 10×, 50× and 100× coverage. The simulation included 5 million 250 bp paired-end background reads. In parenthesis we show the value at each of JAFFA’s classifications levels: (high/medium/low) confidence.