mothur

Using Mothur data for Phyloseq

Dear readers,

I want to use data from Mothur and use Phyloseq for visualization.
I follow the tutorial from Phyloseq: https://norwegianveterinaryinstitute.github.io/BioinfTraining/phyloseq_tutorial.html

It uses
sharedfile = “MiSeq_SOP/final.shared”
taxfile = “MiSeq_SOP/final.0.03.taxonomy”
treefile <- “MiSeq_SOP/final.0.03.rep.otu.phylip.tre”
mapfile = “MiSeq_SOP/mouse.dpw.metadata”

So, I assume the files are:

Sharedfile= stability.opti_mcc.0.03.subsample.shared
taxfile= stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.opti_mcc.0.03.cons.taxonomy
treefile=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.phylip.tre
mapfile= mouse.dpw.metada

That looks right, but I’ve never used phyloseq so I can’t say.

Thanks! But usually what software/program do you usually use for visualization aside from R Package?

I use R. There’s no need to use phyloseq to make plots in R. I have a lengthy tutorial built around using R for generating visuals and doing analysis of microbiome data. The materials are free and I use them to teach my workshops.

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