Should I trim the primers for dada2 workflow?

[danielsangarci]

Hi @benjjneb

I am using dada2 to perform my 16S V3-V4 bioinformatics. I read dada2 require trimming the primers for a correct workflow, but I was said not trimming the primers is better because you have extra information in the sequences. Is it actually correct if I leave the primers in my sequences? If not I will remove them using Cutadapt.

Thank you so much in advance,
Dani

[benjjneb]

Yes you should trim primers if they are present on the sequencing reads. They are not extra information -- the primer sequences are put in by the experimenter, they do not come from the sample.

If, as is usual, primers are at the start of your reads and a fixed length, filterAndTrim(..., trimLeft=c(FWD_PRIMER_LEN, REV_PRIMER_LEN)) is the recommended way to remove them. cutadapt is a fine alternative though.