Table 1 Sensitivity and PPV comparison between methods on datasets simulated assuming uniform, respectively geometric expression of transcripts, with reads length 400 bp, mean fragment length 450 bp and 10% standard deviation.
From: Transcriptome assembly and quantification from Ion Torrent RNA-Seq data
Transcript expression | Methods | # assembled transcripts | # confirmed annotated transcripts | Sensitivity (%) | PPV (%) |
|---|---|---|---|---|---|
Uniform | Cufflinks | 18,582 | 12,909 | 51.06 | 69.47 |
| Â | MaLTA | 23,706 | 18,698 | 76.69 | 78.87 |
| Â | IsoLasso | 21,441 | 15,693 | 63.52 | 73.19 |
Geometric | Cufflinks | 17,377 | 12,449 | 50.21 | 71.64 |
| Â | MaLTA | 22,931 | 18,293 | 76.05 | 79.77 |
| Â | IsoLasso | 20,816 | 15,308 | 62.83 | 73.54 |