Table 2 Required input parameters with example values
Parameter | Value |
|---|---|
1. Total number of profiles | 6 |
2. Number of samples | 3 |
3. Number of replicates per sample | 2 |
4. Number of T-RFs | 3 |
5. Sample names on row | 1 |
6. Consider T-RF if present in X replicates. X= | 2 |
7. Align T-RFs with a size difference shorter than Y bases. Y= | 1 |
8. Add T-RFs less than Z bases longer than the average size of the alignment. Z= | 0.5 |
9. Peak height detection threshold. PDT = | 50 |
10. Lower T-RF Size Limit | 50 |
11. Upper T-RF Size Limit | 1020 |
12. Fixed percentage threshold. FPT= | 0.01 |