I thought that DADA2 (in QIIME2) analyze each sample seperately (with default hyperparameters). However, when I analyzed the "sample A" only, the result was different from the result when I analyzed the "sample A" with other samples.
I checked dada2 status and found that values in the 'merged' and 'non-chimeric' columns were dfferent between those two results (merged values were different by 1, and non-chimeric values were different by ~2000).
So, I checked the dada2 document, and found that using --p-chimera-method "consensus" (default), "chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed". Is that a reason why I got the different result when I analyzed sample A with other samples?
Also, the result from analyzing sample A with other samples gave me less non-chimeric sequences. However, I got more sequences assigned to Prevotella (vsearch, top-hit-only) than analyzing sample A only. How could it happen? The result was quite opposite as I expected, because I thought that all sequences from analyzing sample A with other samples were included in the sequences from analyzing sample A only (just removing more chimeric sequences)...
Thanks for reading!