I’m a beginner in QIIME 2 and currently learning to run the analysis on my own and never been trained professionally in this analysis. Currently, I have paired-end sequencing data and I’m unsure at which position I should truncate my reads. I have 15 samples, and the expected amplicon size is 422 bp. The sequences have already been cleaned by trimming barcodes and primers. Could you please suggest the best forward and reverse truncation lengths so that I can proceed with the denoising step?
Welcome to the forum!
I would start with and compare:
- No truncation
- Truncate reverse reads at position 215 or 210
If the final percentage of reads is pretty low, I would try to:
- Increase max_ee to 5
- Decrease the minimum overlap to 10
There is no penalty for trying! You can play with DADA2 settings and run multiple combinations to see how they change depending on the parameters you choose.
Good luck,
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