Why it is so not intuitive?

“Next, we’ll need to modify the exported taxonomy file’s header before using it with BIOM software.”

why it is so not intuitive?
generation of “a classic otu table” is the main goal of every 16S rRNA experiment, why I need to change something manually…

1 Like

You don’t need to change anything manually. A very simple bash script, for example, would do the conversion you are referring to if you want to do this programmatically.


sure I can write a simple Bash/R/Python/Perl script but why would I like to do it. I hoped Qiime2 is robust enough that will cover the most of the basic user’s needs.
(ok, now I know it’s implemented, but I needed to Google this solution)

qiime taxa collapse --i-table otu-table-flt.qza --i-taxonomy gg_v34_classification_taxonomy.qza --p-level 2 --o-collapsed-table out.taxa
#Saved FeatureTable[Frequency] to: out.taxa.qza
qiime tools export --input-path out.taxa.qza --output-path exported
#Exported out.taxa.qza as BIOMV210DirFmt to directory exported
biom convert -i exported/feature-table.biom -o feature-table.tsv --to-tsv

(feature-table.tsv - this is for me a “classic OTU table” )



Thanks for clarifying your question, @thedam

Your initial question was very vague and quoted an unrelated section of that tutorial (covering metadata annotation of biom-format tables, not conversion of BIOM to TSV).

If you had asked “how do I convert a biom-format table to a ‘classic’ OTU table (TSV)?” I could have provided the answer you were after. But I’m glad Google could yield the answer you needed!

Good luck.


yeah, Qiime2 terminology and data format types are confusing for newbies:)

1 Like