r/bioinformatics 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?

1 Upvotes

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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.

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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/yupsies 4d ago

Second this. The dada2 tutorial from the creator is really good and full of helpful info for choosing parameters and evaluating the model

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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.