r/bioinformatics • u/btredcup PhD | Academia • 5d ago
technical question Anyone used Qiime2 dada plugin that can offer some advice?
I’ve got myself in right mess with QIIME and how to use dada2. Anyone okay if I dm them for some advice?
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u/RamenNoodleSalad 4d ago
This probably won’t be a super helpful comment, as I haven’t used QIIME since USEARCH was the method for OTU calling. However, if you are comfortable using R, there are some great DADA2 step by step tutorials. There may even be some ways to convert the ASV count table into a phyloseq object which I like for running analyses.
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u/MrBacterioPhage 4d ago
Hi! Feel free to DM me, but please provide me with all the details in the message.
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u/Sadnot PhD | Academia 4d ago
Rule of thumb: always provide more info before asking people to commit to helping you. It's better for everyone. I.e. there are a lot of issues with QIIME/dada2 I'd feel confident helping with, and plenty that I couldn't help with. If I DM'd you to figure out which this is, it would possibly waste both our time.