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nickallsing / TJ_River_Project

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Scripts for qiime analyses for alpha rarefaction #2

Closed EugeneMwanza closed 2 months ago

EugeneMwanza commented 6 months ago

Hi @nickallsing @nallsing-salk Very interesting research you guys did. I was trying to replicate your methodology but then I figured there were no qiime analysis scripts. I managed to import the modified OTU table to qiime but I have trouble running the alpha rarefaction part as it requires a phylogenetic tree and I was wondering how you guys did it. Did you have a phylogenetic tree? Because Kaiju doesn't provide one. Please advise on what to do and help with the qiime scripts a swell.

nallsing-salk commented 5 months ago

Hello and thank you for checking out these scripts! I believe that for the core alpha diversity metrics a phylogenetic tree is not required. I would suggest checking out the Qiime2 Moving Pictures Tutorial. It has examples of analyzing alpha and beta diversity.