How to clean taxonomy file for microbiome analysis in R?

Question

[Amr]

How to clean taxonomy file for microbiome analysis in R? should column names be changed? If yes what should be done? I want to perform

[andres.firrincieli]

That is not a taxonomy file.

This is what a taxonomy file looks like (row names d__denovoXXX are the OTU/ASV ID):

## Taxonomy Table:     [5 taxa by 5 taxonomic ranks]:
##               Domain        Phylum             Class            Order              Family              
## d__denovo1773 "k__Bacteria" "p__Bacteroidetes" "c__Bacteroidia" "o__Bacteroidales" "f__Bacteroidaceae" 
## d__denovo1771 "k__Bacteria" "p__Bacteroidetes" "c__Bacteroidia" "o__Bacteroidales" "f__Bacteroidaceae" 
## d__denovo1776 "k__Bacteria" "p__Firmicutes"    "c__Clostridia"  "o__Clostridiales" "f__Ruminococcaceae"
## d__denovo1777 "k__Bacteria" "p__Bacteroidetes" "c__Bacteroidia" "o__Bacteroidales" "f__Bacteroidaceae" 
## d__denovo1775 "k__Bacteria" "p__Firmicutes"    "c__Clostridia"  "o__Clostridiales" "f__Lachnospiraceae"

[Amr]

I guess its a taxonomy file but before cleaning

[andres.firrincieli]

I guess its a taxonomy file but before cleaning

No! It looks like a transposed ASV/OTU count table were the ASV/OTU id were replaced the corresponding taxonomic string.

[Amr]

So you mean that is an ASV file ? because I have the ASV file

[andres.firrincieli]

where did you get this file? You should already have ASV/OTU count table, and a taxonomy file that look like the one I posted in my previous comment.