So, I am analysing 18S amplicon data (fastq files) to be able to eventually investigate the taxa composition.
After removing primers (using
cutadapt) from both R1 and R2 (assuming primers are found at the beginning of my sequences), I am still able to detect, apparently at random, a few reads that contain my primers (i.e. a part of the sequence matching the primer) in, again apparently random, positions.
I am able to detect almost all my primers (16 out of 24, both forward and reverse) in at least one sequence and I am wondering how common (or how weird) this is. I guess it is important to consider that my primers contains a few, i.e. from 1 to 3, wild-card bases that may match multiple other bases (apparently called whobble bases), which makes it easier to match a random sequence (there are multiple possibilities for an actual match).
Problem is that the presence of primers in the sequences may affect downstream analyses (e.g. with DADA2 they are very clear about the fact that primers have to be removed) in several ways and I was wondering if these sequences I am finding may be interfering somehow of if I can live with it.