Table 2.
F-measure [in %] for spliced reads with different number of spanned junctions for simulation 1
| Program | Number of junctions spanned | ||||
|---|---|---|---|---|---|
| 1 (13808336) | 2 (598297) | 3 (11781) | 2* (548382) | 3* (6908) | |
| CM Bwt1 | 91.47 | 14.24 | - | 15.16 | - |
| CM Bwt2 | 94.03 | 78.47 | 50.21 | 82.37 | 72.66 |
| CM Bwa | 95.03 | 82.73 | 53.33 | 86.67 | 76.46 |
| CM Bwa ann | 95.74 | 84.65 | 53.9 | 88.47 | 76.79 |
| MapSplice 2 | 92.42 | 79.18 | 27.27 | 80.65 | 3.44 |
| STAR 1-pass | 77.63 | 30.91 | 5.01 | 31.91 | 1.49 |
| STAR 1-pass ann | 93.55 | 81.65 | 75.71 | 82.57 | 82.17 |
| STAR 2-pass | 95.0 | 85.55 | 82.07 | 86.59 | 87.29 |
| STAR 2-pass ann | 95.07 | 86.28 | 82.55 | 87.02 | 86.49 |
| TopHat1 | 87.83 | 77.51 | 63.57 | 80.42 | 75.56 |
| TopHat1 ann | 88.02 | 78.99 | 68.13 | 81.06 | 76.1 |
| TopHat2 | 91.71 | 87.0 | 76.92 | 89.66 | 88.51 |
| TopHat2 ann | 94.84 | 90.79 | 85.92 | 92.05 | 90.35 |
| GSNAP | 83.13 | 43.45 | 18.52 | 42.35 | 12.29 |
| GSNAP ann | 96.47 | 88.59 | 79.51 | 89.86 | 84.67 |
*The last two columns show results only for reads for which all exons except the first and last exon had length ≥ 20 nt. For this evaluation, read alignments were only considered a true positive if all simulated splice junctions in the read were recovered and no additional splice junctions were identified. Indels were ignored for this purpose. Recall and precision values for both simulations can be found in Additional file 1: Table S5.