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!

1 Like

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
Luca

3 Likes

Hi Luca! It makes perfect sense. Thank you!

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