The parameters i used were the following
since I don't have the adapters sequences but the lenght (barcodes + adapters), I used that parameter to cut.
qiime dada2 denoise-paired
The results I obtained were
vs the results using only the forward sequences
As you can see, using both forward and reverse I end with 26,855 vs 40,361 using only the forward sequences, this is a huge difference when I assign taxonomy.
I am not sure if I'm cutting too much or I'm not cutting enough or I'm missing something.
Thanks in advance !