Confusion about Singleton after DADA2

[zhonglin_ma]

Dear all,
I want to know does singletons will be removed automatically after denoising by DADA2? And how many percent it would be generally? my dada2 denoise result shows that there are 49.65% of seqs and 75.3% of clusters(97% similarity) Singleton, does it acceptable?

[jwdebelius (Justine Debelius)]

Hi @zhonglin_ma,

EDIT: Deblur removes any read with fewer than 10 counts by default; Dada2 removes anything with less than 2 counts by default. (I apologize for the confusion.)

Have you gone forward with OTU clustering at 97% which has resulted in singletons? (I typically think of singleton as 1 count, are we talking about the same thing?)

And, I think the general answer of “is it acceptable” depends a lot on the context.

Best,
Justine