Truncate/denoise with dada2 and trim with cutadapt: (how) can I do it?

Hello everyone

I've had some issues with my sequences primers and was advised to trim them using cutadapt instead of dada2, and I did that. Then I remembered I was also told that truncation is done before trimming, but that was back when I was going to trim with dada2, and both trimming and truncation would all be done in one code. That left me with a few questions I can't seem to answer by looking at previous topics from the forum:

  1. Can I trim the primers using cutadapt and truncate/denoise using dada2?

  2. Can I first trim with cutadapt and then truncate/denoise/filter with dada2?

  3. If truncation needs to be done first, and I truncate with dada2 before trimming with cutadapt, won't the dada2 truncation code also do denoise and filter by default, before I get a chance to trim the primers?

First I thought I could just truncate and trim using cutadapt, but it looks like it doesn't allow truncation using bp position, only using the sequence itself.

Sorry if I made a mess with the concepts, I'm still trying to understand all of that. I appreciate any help you can give me!

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Hi @microbiotaphyto,

I think that who told you about trimming/truncation order was referring to the steps performed by dada2.
You definitely can trim your primers off by using q2-cutadapt, then you need to use q2 demux summarise to identify the best trimming position to use in dada2 after trimming your primers.

Hope it makes sense


Hi Luca! It makes perfect sense. Thank you!

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