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:
Can I trim the primers using cutadapt and truncate/denoise using dada2?
Can I first trim with cutadapt and then truncate/denoise/filter with dada2?
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!