high chimera rate in dada2

[Nicholas_Bokulich]

@Claire010

My situation is the majority of merged ASVs are inferred as chimera, but they account for 19% of merged reads.

Oh I see, I think I misread this above... 19% is not super high, I agree you can probably just "move on" especially since you have very high read depth.

@Claire010

However, in my opinion, as long as the chimera doesn’t affect the microbial composition and the sequencing is deep enough to cover most of the diversity (Chao1 and rarefaction reached a plateau), we can still go on with the analysis after removing chimera.

I agree, with the significant change that chimera is chimera, and (assuming the chimera checker is not grabbing false positives) should be removed whether or not it changes the results! Of course there's the valid question of whether the chimera checker is accurate, and I cannot help there, I recommend looking at the benchmarks in the literature for that method if you want to assess overall accuracy...

@Claire010

PS: my only concern is whether a relatively high proportion of chimera (such as 20% of reads are chimeras) would change the bacterial community? I could not find a paper discussing on this. If there is, please correct me.

Removing chimera would probably change the taxonomic results, but this is good and intentional if the chimera really are a PCR artifact and do not represent true diversity in your samples. So I recommend just "moving on" since your chimera rate is not all that high.

Good luck!