loss of reads after DADA2 as chimeras

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Hi @Shruthi,
70% is indeed quite a bit, hopefully we can improve on that a bit. Here are some things to consider and follow up questions:

  1. Your trim/truncating parameters look good to me, with plenty of overlap for merging etc. however,
  2. DADA2 can struggle a bit with chimera detection if non-biological sequences are left in your reads, for example if you haven’t removed your adapters, barcodes, primers etc. So this is a good starting point to make sure you only have biological sequences in your reads.
  3. On the wet lab side of things, how many PCR cycles did your samples go through? Did you use a high fidelity polymerase? These can often affect chimera production.
  4. Lastly, you can try adjusting the --p-min-fold-parent-over-abundance parameter in dada2.
  5. The good news is that even if for some reason you do have lots chimeras being removed your output is still very good and with the exception of 1/2 samples you could easily just move on and not worry too much about them.
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