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How to clean taxonomy file for microbiome analysis in R?

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

taxonomy microbiome_analysis
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written by Amr • Amr

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"
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written by andres.firrincieli andres.firrincieli

I guess its a taxonomy file but before cleaning

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written by Amr • Amr

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.

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written by andres.firrincieli andres.firrincieli

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

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written by Amr • Amr

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.

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written by andres.firrincieli andres.firrincieli

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