Dear Friends,
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?
Thankks
Hi @Mehrdad,
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.
Best,
Justine
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Thanks Justin!
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?
Hi @Mehrdad,
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.
Best,
Justine
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