adapters 16s

[murheisa]

Hello, I´m working with some 16S v3-v4 sequences with Miseq 300pb, 200k reads per library. The sequencing service says they do not process de sequences for adapter removal. I checked with fastqc and apparently there are no adapters (Nextera), and after dada2, I checked for primer removal and indeed the primer was removed, but what about the adapters? One of my samples appear to have too many ASVs and overrepresented sequences with no hit in fastqc, so I thought that could be the adapter even if it does not appear in fastqc. Also in that sample, half of the reads were removed as chimeras, and still has a lot of ASVs. I tried trimmomatic to remove adapters in case there where but I'm not sure if it makes sense to do it. I don't know how to proceed, please help.

These are the parameters I used for filter and trim : filterAndTrim(fnFs,filtFs,fnRs,filtRs, truncLen=c(270,210),maxN=0,trimLeft=c(10,10), maxEE=c(2,2), truncQ=2, rm.phix=TRUE,compress=TRUE, multithread=TRUE) #

rarf_2.pdf rarf_2.pdf