Cutadapt trim-paired vs. dada2 (option --p-trim-left)? Help with interpretation of cutadapt output.

Hi @jul!

Sorry for the slight delay on our part.

You are indeed understanding the output of cutadapt correctly. There are some things you might be interested in which can change the trimming behavior:

According to this table (--p-front-* maps to -g in q2-cutadapt), you can use a starting character ^ to anchor exactly at the beginning, or X to anchor “not-exceeding” the beginning.

That said, I suspect your primer isn’t of variable length here, so using trim-left in DADA2 is definitely much easier in this case (and it lets you avoid sequencing error slipping through!) so I would probably recommend that, just as you were thinking.

2 Likes