Congrats for the great job with qiime2! It works perfectly for ITS single end, but we couldn't find any tutorial for QIIME2-ITS using dada2 and pair-ended reads. The original dada2 tutorial has a different syntax (DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution). What would be the command to run ITS data using dada2 and pair-ended reads in QIIME2, since we shouldn't trim the sequences because of the length polymorphism? Are you aware of any tutorial that successfully used QIIME2 for ITS using pair ended reads? Or could you please post a tutorial like that, perhaps using the data from the benjjneb.github.io? thanks a lot!
Here is the original tutorial/data from dada2: DADA2 ITS Pipeline Workflow (1.8) . We were wondering if anyone could run the same example using QIIME2. The syntax is different and we shouldn't trim sequences because of length polymorphism - how could we run the same example in qiime2?
Hello Michael,
Welcome to the forums! 
As a starting point, try swapping the dada2 step in that tutorial for
qiime dada2 denoise-paired
https://docs.qiime2.org/2022.2/plugins/available/dada2/denoise-paired/
You may still want to trim to remove low quality base pairs in the area of overlap. You are correct that the variable length region makes variable length of overlap, and overlap under --p-min-overlap would cause reads not to join and could introduce bias.
Try it and see how it run.
(If you included any positive controls, you could use these to validate the paired end pipeline.)
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