Table 1.
RNA-seq data used to test TopHat-Fusion
| Data source | Sample ID | Read type | Fragment length | Read length | Number of fragments (or reads) |
|---|---|---|---|---|---|
| Edgren et al. [12] | BT474 | Paired | 100, 200 | 50 | 21,423,697 |
| Edgren et al. [12] | SKBR3 | Paired | 100, 200 | 50 | 18,140,246 |
| Edgren et al. [12] | KPL4 | Paired | 100 | 50 | 6,796,443 |
| Edgren et al. [12] | MCF7 | Paired | 100 | 50 | 8,409,785 |
| Maher et al. [11] | VCaP | Paired | 300 | 50 | 16,894,522 |
| Maher et al. [11] | UHR | Paired | 300 | 50 | 25,294,164 |
| Maher et al. [11] | UHR | Single | 100 | 56,129,471 |
The data came from two studies, and included four samples from breast cancer cells (BT474, SKBR3, KPL4, MCF7), one prostate cancer cell line (VCaP), and two samples from the Universal Human Reference (UHR) cell line. For paired-end data, two reads were generated from each fragment; thus, the total number of reads is twice the number of fragments.