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.