Table 4.
Accuracies obtained from RNA-Seq data sets with various properties
| Species | Seq. Error | Read type | Read length | Read number (×106) |
Throughput (MB) |
MPE | 10% EF | FP |
|---|---|---|---|---|---|---|---|---|
| M | N | SE | 35 | 20 | 700 | 3.1/4.2/7.1 | 13.7/25.0/44.0 | 1.0/1.8/10.9 |
| M | N | SE | 70 | 20 | 1400 | 3.1/4.1/6.0 | 13.6/23.9/40.4 | 0.8/1.5/8.2 |
| M | N | PE | 35 | 20 | 1400 | 3.0/3.9/4.9 | 13.3/21.9/34.2 | 1.1/1.8/13.4 |
| M | N | SE | 35 | 40 | 1400 | 2.3/3.1/4.8 | 8.4/18.5/35.8 | 0.7/1.3/10.5 |
| M | Y | SE | 35 | 20 | 700 | 3.1/4.2/6.9 | 14.1/25.2/43.0 | 1.1/1.9/13.2 |
| M | Y | SE | 70 | 20 | 1400 | 3.0/4.0/6.0 | 14.2/24.4/40.6 | 1.1/1.6/9.5 |
| M | Y | PE | 35 | 20 | 1400 | 3.0/3.9/5.1 | 14.0/22.9/35.5 | 1.3/1.9/12.1 |
| M | Y | SE | 35 | 40 | 1400 | 2.2/3.0/5.0 | 8.5/18.4/35.7 | 0.9/1.5/11.3 |
| H | N | SE | 35 | 20 | 700 | 4.0/7.8/14.3 | 20.2/43.5/58.6 | 3.6/8.0/21.6 |
| H | N | SE | 70 | 20 | 1400 | 3.9/7.3/11.9 | 19.3/41.0/54.4 | 3.5/7.0/17.3 |
| H | N | PE | 35 | 20 | 1400 | 3.7/6.2/9.0 | 17.0/36.4/47.3 | 3.7/6.4/14.0 |
| H | N | SE | 35 | 40 | 1400 | 2.9/5.7/10.1 | 13.4/35.4/50.3 | 2.7/6.3/20.3 |
| H | Y | SE | 35 | 20 | 700 | 3.9/7.7/14.8 | 19.5/43.2/59.3 | 3.9/8.1/20.8 |
| H | Y | SE | 70 | 20 | 1400 | 3.8/7.2/12.4 | 19.2/40.8/55.2 | 3.9/7.1/17.7 |
| H | Y | PE | 35 | 20 | 1400 | 3.8/6.5/9.2 | 19.0/37.8/48.2 | 4.2/6.4/13.9 |
| H | Y | SE | 35 | 40 | 1400 | 2.9/5.6/10.3 | 12.8/35.5/50.8 | 3.0/6.3/18.8 |
Accuracy of abundance estimates from RNA-Seq data sets varying in species (H = human, M = mouse), sequencing error, type (SE or PE) of reads, number of reads, and length of reads. Values are given as gene/global isoform/within-gene isoform.