TABLE 5.
Benchmark of sample 33G-30 versus CHESS
| Feature | Parameter set | Recall | Precision | F1 |
|---|---|---|---|---|
| Transcript | Conservative | 23.6 | 49.6 | 32.0 |
| Transcript | conservative_trimming | 23.6 | 49.4 | 31.9 |
| Transcript | Default | 24.2 | 46.0 | 31.7 |
| Transcript | default_noguide | 9.7 | 38.9 | 15.5 |
| Transcript | Mix | 22.7 | 52.7 | 31.7 |
| Transcript | mix_noguide | 11.2 | 55.7 | 18.7 |
| Exon | conservative | 49.7 | 77.0 | 60.4 |
| Exon | conservative_trimming | 49.8 | 76.9 | 60.5 |
| Exon | Default | 50.4 | 75.0 | 60.3 |
| Exon | default_noguide | 39.0 | 79.8 | 52.4 |
| Exon | Mix | 49.4 | 80.3 | 61.1 |
| Exon | mix_noguide | 40.0 | 86.8 | 54.8 |
| Intron | conservative | 49.8 | 88.7 | 63.8 |
| Intron | conservative_trimming | 49.9 | 88.7 | 63.9 |
| Intron | Default | 51.1 | 86.0 | 64.1 |
| Intron | default_noguide | 47.3 | 87.4 | 61.4 |
| Intron | Mix | 51.2 | 93.4 | 66.1 |
| Intron | mix_noguide | 46.2 | 95.4 | 62.3 |
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Parameter sets: default: StringTie with default parameters. noguide: StringTie run without reference. Conservative: uses the ‐‐conservative flag (same as -t -c 1.5 -f 0.05). trimming: enables trimming (-t flag). mix: uses mix for combining Illumina and Nanopore reads. Bold entries represent the top metric for each feature group.
