How to clean taxonomy file for microbiome analysis in R?
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10 weeks ago
Amr ▴ 140

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 • 320 views
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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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I guess its a taxonomy file but before cleaning

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

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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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