Table 1.
Top 10 pipelines based on the overall precision and accuracy ranking.
| Ranking | Trimming method | Alignment method | Counting method | Normalization method | Median precision | Median accuracy | Median overall precision and accuracy |
|---|---|---|---|---|---|---|---|
| 1 | Trimmomatic | RUM | HTSeq UNION | TMM | 68.5 | 56 | 249 |
| 2 | Trimmomatic | RUM | HTSeq INTER | TMM | 68.5 | 57.75 | 252.5 |
| 3 | BBDuk | RUM | HTSeq UNION | TMM | 70 | 56.5 | 253 |
| 4 | BBDuk | STAR | HTSeq UNION | TMM | 68 | 62 | 260 |
| 5 | Cutadapt | TopHat2 | HTSeq UNION | TMM | 62.5 | 67.75 | 260.5 |
| 6 | BBDuk | TopHat2 | HTSeq UNION | TMM | 63.5 | 68 | 263 |
| 7 | BBDuk | HiSat2 | HTSeq UNION | TMM | 63.5 | 69.25 | 265.5 |
| 8 | BBDuk | TopHat2 | HTSeq INTER | TMM | 62.5 | 70.5 | 266 |
| 9 | Trimmomatic | STAR | HTSeq UNION | TMM | 69 | 64.75 | 267.5 |
| 10 | Trimmomatic | STAR | HTSeq INTER | TMM | 63.5 | 71 | 269 |
The lower the median overall precision and accuracy the better the pipeline performance was.