I do not have much experience with Qiime2, could anyone help me?
I have read a lot about this discussion, and I realized that there is no consensus, but I still would like the opinion of you, who certainly have more experience in Qiime2 / microbioma than I do.
I have 3 sequential negative controls, and I thought about filtering / deleting all the ASVs that appeared on the three negative controls or if it appeared in only one but had a high amount of reads (over 500), but I believe that this way I I am deleting an important part of my data. Anyone have any suggestions?
I agree. There is indeed no consensus on the “best” methods. If there is any consensus, though, it is that filtering out anything found in negative controls by default is a bad idea. See this discussion for more details: