Table 3. Summary of DTU features (genes or transcripts) detected by each method.
DRIM-Seq reports DTU only at the gene level. SUPPA2 reports DTU only at the individual transcript level. RATs reports at both the transcript and the gene levels, using its respective test implementations. For SUPPA2 and the transcript-level approach in RATs, gene-level results can be inferred from the reported transcripts; these are included in the table, enclosed in parentheses. The last two columns show the reproducibility of the results between annotation versions. DTU: Differential transcript usage.
|
RATs
(genes) |
RATs
(transc) |
RATs
(tr. aggr.) |
SUPPA2 |
SUPPA2
(tr. aggr.) |
DRIM-Seq | |
|---|---|---|---|---|---|---|
| RATs (genes) | - | 97% | - | 46% | 19% | |
| RATs (transc.) | - | - | 35% | - | - | |
| RATs (tr. aggr.) | 78% | - | - | 42% | 17% | |
| SUPPA2 | - | 53% | - | - | - | |
| SUPPA2 (tr. aggr.) | 42% | - | 49% | - | 17% | |
| DRIM-Seq | 39% | - | 43% | - | 38% |