Title says it all. I'm generating ASVs from several studies' datasets, but some have reads were merged prior to uploading to NCBI or wherever.
My PI tells me that dada2 can't handle this sort of thing (I haven't run through it myself, but I gather that it might obscure the true biodiversity even if dada2 doesn't give a flat-out error). We were going with mothur & vsearch to make OTUs earlier in the process, but mothur doesn't play nice with snakemake and dada2 would be better anyway.
Anyone have any pointers? Help would be very much appreciated!