I have a question. I would like to know after demultiplexing how can I detect the treated and untreated samples in my library? is the step after clustering or it would instantly be after demultiplexing?
You should be doing feature-based comparison on your clustered/denoised feature table. However, you should already know which samples are treated or untreated. Microbiome analysis has to be supervised at the moment.
The library was already demultiplexed, denoised with dada2 and visualized. The metadata which contains barcode sequences and other details are in available.
You pointed out I should follow feature-based comparison. I could not find comparisons item in denosing parameters? Could you please tell me how should I do that?
There have been several feature-based discussions going around, this one is pretty comprehensive and relatively recent. I should note that I use “feature” as a generic term to reference ASVs, OTUs, or whatever you’re representing in the table.
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