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You are not alone! This is hard choice because you are facing a trade-off between keeping more samples or keeping more depth in each sample, and you want to do both!
Check out these discussion of the issue, and let us know what you decide to do
Hi @Alinne_Castro ,
That is a great question! My thoughts on the topic, though I look forward to hearing others’ as well. Sorry about the length of the reply!
The question is rather loaded and I don’t think there is really a simple answer for this, so I’ll touch on a few points that might simplify it a bit.
In my opinion, the most important factor is the sample source. If you are looking at a sample that you expect to have low 16S diversity (for example, a wine sample) then you might get all…
Hi,
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%) sample…
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