hi there,
I am new to bioinformatics for microbiome data. I am currently using Humann3 for shotgun metagenomics. I have successfully run Humann3 on my data and obtained the genefamily, pathabundance tables. I have also run metaphlan on the intermediate bowtie files produced during the humann3 run and merged metaphlan taxonomic tables across samples. I want to conduct downstream analysis for diversity metrics and eventually run GLMMs in R. I have tried looking into what options exist to get humann3 outputs into qiime format and there seems to be several options? I want to know which one is the best way to do it in order to produce objects that can are compatible with R packages like vegan and phyloseq?
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So far I have tried following the code from this paper but the final diversity calculations look off to me. I wasn't sure if unstratified or stratified tables be used for downstream analysis?
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I also tried using the q2-sapienns plugin which worked for my files but I am at a loss as to how to convert the .qza and .qzv files into input files for R phyloseq or vegan packages. This might be a super trivial question - but I feel like I am going into rabbit holes trying to find the answer for this. So would appreciate any feedback from more experienced users!
Thanks in advance!