An unexpected problem arises in the feature table

Why do I use qiime dada2 de-paired to generate a feature table with only one sample for each OTU value, and the other samples are all 0 in the OTU annotation. Does anyone with a good heart know ?

Hello @Xiang,

May I ask why you think this is a problem? Were you expecting greater feature similarity between your samples? Was there a specific feature you were expecting to observe in more samples than you did?

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Because a large number of OTUs in the feature table generated by my other data appear in more than one sample, and I directly use dada2 to generate the feature table in R instead of using dada2 in qiime2 to generate, the final result is also a large number of OTUs appear in more than one sample, so I think this result is somewhat strange. :rofl:

Hello @Xiang,

Are you saying that the same data yielded different tables depending on whether you used dada2 directly or through qiime? If it's not the same data then one wouldn't necessarily expect the differences you're describing to not happen. Maybe you're viewing the two tables at different taxonomic levels? The more specific the taxonomic level the less likely it is that you'll see features shared across samples.

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