I am trying to choose a sampling depth for my table-deblur and table-dada2. Based on what this post How to decide --p-sampling-depth value? says I need to choose a value such that I retain high number of features as well as samples so I capture the true diversity.
I chose 20825 for table-deblur. Using this value I would retained 2,353,225 (60.13%) features in 113 (81.88%) samples.
I chose 38093 for table-dada2. Using this value I retained 4,837,811 (63.93%) features in 127 (92.03%) samples.
2- Looking at these file I noticed that I obtained 3,913,403 feature after runnig Deblur and 7,567,910 after runnig DADA2. I know from previous posts that this difference is due to the way these two methods handle the error. But I am not sure which one is more reliable. Which one should I choose for downstream analysis?
Thank you for your support.