Hi I wanted to ask for your opinion about my filtering approach to remove low abundant ASVs before continuing with the downstream analysis: I rarefied my filter-table at a sequencing depths of 50'000 reads I use the threshold of 10^-4 relative abundance to remove low abundant reads. Hence I u…

Hi there @cla ! [image] cla: Should I rarify again to the the sequencing depths of the sample with the lowest depths after noise-removal? It depends on what you are doing downstream. If you are running a particular metric or method that is sensitive to sampling depth, then yes, you will want …

Thanks for your reply. Is this the standard filtration approach or do you suggest different steps?

[image] cla: Is this the standard filtration approach or do you suggest different steps? Sounds like you are following a qiime1-style OTU filtering protocol . I have some changes to recommend. If you used dada2 or deblur to denoise your sequences, then abundance-based filtering should not be…

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