Program | No. of mapped pairs | Correctly mapped pairs, % | Incorrectly mapped pairs, % | Unmapped pairs, % | Correct junction pairs, %a | Correct short-anchored pairs, %b |
---|---|---|---|---|---|---|
TopHat2 + Bowtie1 | 19,683,426 | 96.70 | 1.72 | 1.58 | 93.31 | 90.09 |
TopHat2 + Bowtie2 | 19,686,006 | 96.19 | 2.24 | 1.57 | 92.03 | 85.88 |
TopHat1.14 | 19,219,055 | 89.57 | 6.53 | 3.90 | 78.36 | 40.39 |
GSNAP | 19,999,867 | 88.84 | 11.16 | 0.00 | 76.55 | 22.87 |
RUM | 19,869,579 | 79.07 | 20.28 | 0.65 | 56.28 | 8.42 |
MapSplice | 19,342,087 | 92.03 | 4.68 | 3.29 | 86.53 | 72.48 |
STAR | 19,951,620 | 85.21 | 14.55 | 0.24 | 68.94 | 3.16 |