Hi, I am running an analysis that combines data from multiple MiSeq runs from different studies. My approach has been to generate ASVs and remove chimeras using the dada2 denoise-paired plugin individually for each plate, and then merge all the resulting ASVs from all plates into one big dateset with feature-table merge-seqs and feature-table merge. However, I just noted that on the big data tutorial on the Dada2 site (A DADA2 workflow for Big Data (1.4 or later)), the chimera removal is done after all the plates are merged. My question is, does it matter if the chimera removal step is done prior or after merging all the ASVs together? As far as I can tell, both the consensus and pooled approaches for --p-chimera-method take some consideration of the larger pool of sequences in the whole plate into account; this leads me to think that perhaps doing chimera removal before or after merging all ASVs from all the plates will produce different results. However, on the other hand, since the different plates usually have samples from different studies/locations on them (although often similar habitats), it doesn't seem like it is going to provide a radically different result if the chimeras are removed prior to merging all ASVs into one dateset. I am curious what others think about this, and whether or not it matters. I have noticed some workflows posted online (e.g., Merging DADA2 Results in QIIME2 - John Quensen) that don't mention chimera removal after merging multiple ASV datasets together, which leads me to think it isn't that important to wait until after merging.
If I did want to run the chimera removal for dada2 after merging all the ASVs together, is there a way to do that with dada2 denoise-paired? I see that there is an option to turn off the chimera removal, which I could do when running each individual plate. However, after merging all the ASVs into one big dataset, is there a way to run the chimera removal function in dada2 denoise-paired without it also doing the actual denoising step? Or, would I need to use one of the other chimera removal tools available in Qiime2?