Thanks for the sleuthing @colinbrislawn!
@Kat, the DADA2 denoise methods remove chimeras by default --- here is the relevant parameter for chimera detection and removal:
--p-chimera-method [pooled|none|consensus]
The method used to remove chimeras. "none":
No chimera removal is performed. "pooled":
All reads are pooled prior to chimera
detection. "consensus": Chimeras are
detected in samples individually, and
sequences found chimeric in a sufficient
fraction of samples are removed. [default:
consensus]
The default method is consensus, which identifies and removes chimeric sequences --- this is probably why you don't have any feature counts of one in your resulting features table (@benjjneb, please correct me if I am wrong!). If you are interested, you could re-rerun your denoising step with --p-chimera-method none, then you can compare the results!
As far as that phyloseq message, I too would be curious to know if that message is still applicable in the world of ASVs, maybe @benjjneb can comment on that? I don't think Paul McMurdie is on this forum (at least not under a username I could find), so your best bet might be to ask these phyloseq questions on the phyloseq support page --- if you do, please report back here on what you learn!
Thanks! 