After processing my 16S rRNA dataset with QIIME2, I am now exploring and analysing the data. I was about to filter ASVs with low overall relative abundance using the method recommended by Bokulich et al. 2013 (with a threshold c = 0.005%).
I noticed that changing this threshold from 0.005% to 0.0005% or 0.0001% was dramatically altering the results (from 569 ASVs retained to 3875 or 9671 ASVs retained). I therefore wanted to ask for advice, as I understand that filtering the data is important to avoid spurious sequences, but I would like to avoid losing too much information?
Also, I came across another discussion saying that it is not necessary to filter the data if dada2 is used for denoising: Alpha-diversity after filtering
Please excuse me if this is a stupid question, I am not sure to understand why abundance filtering is not necessary after processing data with dada2? As I did exactly that, should I actually not be filtering my data?
Thank you so much for your help!