Hi, I have some basic questions about chimera filtering; this might be silly so thanks in advance:
What is a chimera and how does it happen? By the way, if I have a clean .fna file that has the chimera already removed. Once I import, dereplicate and cluster this file, do I still need to do the chimera filtering procedure?
Chimeras in 16s analysis terminology are sequences that actually derived from two different microorganisms. It may happen during PCR step, when some sequences failed to be elongated enough and then were used for another sequence amplification.
If such sequences already removed and you are going to replicate and cluster your sequences (to OTUs?) by vsearch, then you don't need to remove chimeras. For Dada2 workflow I would prefer to use raw data before any processing (except of demultiplexing and adapters removal).
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