Importing ASVs to R (Phyloseq package)

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1

Hi All,

I am new here and to Bioinformatics.

Recently I have analysed some microbial community data. First processing the sequences in QIIME2 following more or less the tutorial (Moving pictures).
So far everything worked fine and I could import the DADA2 taxanomic anotated table to R and work with it there.

Now that I have overview of the microbial profiles from my samples I want to use the Phyloseq package in R which as far as I can see needs 3 output files from QIIME2. Taxonomy, metadata and feature table. The later I have difficulties with.

Appart from investigating the microbial community change (on taxanomic level) I also want to visualise the relative abundance change in ASVs in some microbial groups.

Is there a way to create a table that have the freequences of sequences anotated to the highest taxonomic level possible AND including what ASVs make up those assignment?

Alternatively I could immagine a feature table only with ASVs (not taxonomically assigned) would be enough as imput for the Phyloseq package. I have not worked with this yet so not sure.

Any help is dearly charrished also if anyone knows a good way to import QIIME2 files to phyloseq in R. Thanks in advance.

PS. I am abroad so answers to questions might be slow.

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Hi @OBrodnicke,
Welcome to the forum!
Check out this awesome tool for importing Qiime2 data into R and even directly to phyloseq.

There isn't an option for this in Qiime2 though your taxonomy visualization can easily show which ASVs belong to which group; these don't have the frequencies though. You'd have to customize something in R to accomplish this since its a very specific request. From memory I don't think this exists in Phyloseq either but you might want to ask about that on their github page.

This is in fact the best way to do this in Phyloseq. You provide it with a feature table of ASVs and separately provide your taxonomies then use tax_glom to choose which taxonomic level to analyse your data at within each script.

If you do make a script or find an easy way to accomplish what you described feel free to share it here, would certainly be good to have around!