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Table 2 Required input parameters with example values

From: Tools for T-RFLP data analysis using Excel

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
  1. Parameters 1-5 and 9-11 are used for the initial preparation of the data. Parameters 1-4 are also used by procedures that need the number of samples or replicates to be specified. Parameter 6 is used for the generation of consensus profiles. Parameters 7 and 8 are used in the alignment of T-RF profiles. Parameter 12 is used for normalization with the fixed percentage threshold procedure.