cannot find any document for interpreting out_table

[KE_XU]

Hi, I have a problem with out_table interpretation.
The command line I use is:

Export OTU table

#mkdir phyloseq
#qiime tools export
#--input-path table-dada2.qza
#--output-path phyloseq \

Convert biom format to tsv format

biom convert
#-i phyloseq/feature-table.biom
#-o phyloseq/otu_table.tsv
#--to-tsv
#cd phyloseq
#sed -i '1d' otu_table.tsv
#sed -i 's/#OTU ID//' otu_table.tsv
#cd ../

and the file of out_table.tsv is

I want to know about the first colume. How could I know each id stands for what?

Thanks in advance.

[jwdebelius (Justine Debelius)]

Hi @KE_XU,

The first column is the feature ID. The OTU/biom representation is transposed, so features are rows and samples are columns. You can get the taxonomic assignment from the taxonomy artifact, and the sequence from summarizing the representative sequences.

Best,
Justine

[KE_XU]

Thanks for your help!

How could I get what you said "the taxonomic assignment from the taxonomy artifact, and the sequence from summarizing the representative sequences."?

Thanks in advance.

[jwdebelius (Justine Debelius)]

Hi @KE_XU,

You can generate a summary of the features in :qiime2: following the feature table summary section of the moving pictures tutorial or just by exporting the data.

An example of naive baysian taxonomic classification is also available from the moving pictures tutorial, but I reccomend also looking into the q2-feature-classifier, q2-clawback and RESCRIPt.

Best,
Justine