Table 1. Comparison of reference-based approaches.
| Program combination | vs. orthology annotation | vs. EST annotation | ||
| Base-level accuracy (%)1 | Confirmed junctions (%)1 | Base-level accuracy (%)1 | Confirmed junctions (%)1 | |
| TopHat + Cufflinks | 83.9 | 75.8 | 68.9 | 63.0 |
| GSNAP + Cufflinks | 79.4 | 71.2 | 65.7 | 58.4 |
| GSNAP + Cufflinks (subsample2) | 80.3 | 72.7 | 60.2 | 66.3 |
| TopHat + Scripture | 70.3 | 67.9 | 60.8 | 62.5 |
1Base level accuracy and percentage of confirmed junctions with different combinations of mapper and assembler on the sample ps94 males compared to the orthology annotation and the EST annotation (2based on 48 M reads).