I was recently analyzing a data set of 16S V3V4 amplicons (from soil samples) and was running them through the DADA2 pipeline. I was losing 30-45% of my sequences in the chimera filtering step, and according to Dr. Callahan's DADA2 tutorial, that's way too high of a percentage.
One of my lab mates told me that she's read that losing ~30% of your reads to the chimera filtering step in DADA2 and/or QIIME is normal when it comes to environmental microbiomes, but I am having a hard time finding that information in the literature.
My question is: if you've sequencing envrionmental microbiomes, have you lost a high % (>5% according to the DADA2 tutorial) of reads to the chimera filtering step? Is this common with environmental microbiomes as opposed to a gut microbiome (for example)?
Thank you for your input!
From the top of my head, in general at most 5% is lost to chimera detection. However, if you don't trim the PCR primers, then the proportion is a lot higher.
Are you properly trimming out the PCR primers? How?