Convert biom to tabular file and parse taxonomic levels

Question

[naphtali.paul]

Hi all,

I currently have an otu table that was generated from QIIME in the biom format. It comprises of 16S rRNA sequences that were annotated into OTUs. I used the biom convert command to create a tsv file, but the taxonomy names follow the Greengenes guidelines, where taxonomic levels are identified by k__(name); p__(name), and so forth to s__; , the species level.

Is there a flag within the biom commands which lets me parse the taxonomic levels as separate columns in the tsv file? I'm doing this so I can input the tsv table into R to analyze the data with vegan.

Thanks!

Answer 1

[lakhujanivijay]

Did you try this?

> biom convert -i table.biom -o table.from_biom_w_taxonomy.txt --to-tsv --header-key taxonomy

Also, please let me know the exact command you are running.

Answer 2

[fanli.gcb]

If you are doing 16S analysis with R, you may want to check out the phyloseq package. It has built-in functions for parsing QIIME biom files as well as many other things you'll likely want to do. See https://joey711.github.io/phyloseq/import-data.html#import_biom