Hi, I'm working on my first major QIIME run and I have few questions about the best format for the pipeline. I see the examples online, but I was given an example that differs quite a bit and I wanted to know some opinions on which way I might have a more successful outcome. Current Pipeline: Im…

Hi @reige012 , Is there a specific reason why you have to include Vsearch at all? Is OTU clustering really needed for your project? I ask because you are already utilizing dada2 to create ASVs which are just higher resolution analogues of OTUs. In most cases, there is no more needed for OTUs. I woul…

[image] reige012: rarefy samples and make new feature table You do not need to rarefy either — rarefied tables should only be used as input for alpha/beta diversity methods, and this is automatically built in to the core-metrics pipeline. Do not use rarefied tables for differential abundance…

Thank you for your thoughts. These are both very useful comments.

I do have another questions in regards to these responses. Is there a way to essentially "clean" and trim the sequences without using dada2 so that I can then cluster into OTUs instead of ASVs? I'd like to do both OTU (99% and 97%), as well as ASVs to see if there are any differences in the final ou…

See q2-quality-filter to perform qiiime1-style quality filtering . [image] reige012: I’d like to do both OTU (99% and 97%), as well as ASVs to see if there are any differences in the final outcome. There will be vast differences. Unless if you use a mock community (as the dada2 developers did…

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