Table 2.
Linear regression slope and lowest limit of detection (LLD) for observed transcripts per million (TPM) and expected ERCC concentration values in the three datasets: human cell lines (Homo sapiens), Arabidopsis (Arabidopsis thaliana) and zebrafish (Danio rerio)
| Dataset | Homo sapiens | Arabidopsis thaliana | Danio rerio | |||
|---|---|---|---|---|---|---|
| pipeline settings | Slope | LLD | Slope | LLD | Slope | LLD |
| star+salmon | 0.96 | 3.81 | 0.96 | 4.11 | 0.93 | 7.14 |
| star+rsem | 0.96 | 3.88 | 0.96 | 4.41 | 0.95 | 6.89 |
| star+featureCounts | 0.96 | 18.5 | 0.97 | 4.48 | 0.95 | 7.75 |
| hisat+featureCounts | 0.96 | 17.6 | 0.97 | 4.56 | 0.95 | 6.72 |
| pseudoaligner salmon | 0.96 | 3.78 | 0.96 | 4.05 | 0.92 | 6.81 |