April 6, 2022, 9:00pm
I am trying to a taxonomy table.txt to qza format, of which a final goal is to make my own classifier.
The first step, as far as I learned in this forum, is to convert txt to biom file.
Using taxonomy table (see below), i converted txt to biom format with command:
"biom convert -i dsrB-taxonomy.tsv -o dsrB-tax.biom --table-type "OTU table" --to-hdf5"
That command resulted in creating dsrB-tax.biom in my qiime folder.
Q1: is the command right? I don't know why the table-type is "OTU table"
Q2: is there a way to check out if the biom is correctly made as taxonomy table?
I would appreciate any comment and/or advice..
April 6, 2022, 9:17pm
To import taxonomy into the Qiime2, you do not need to convert it to the biom format.
qiime tools import \
--type 'FeatureData[Taxonomy]' \
--input-path taxonomy.tsv \
April 6, 2022, 10:45pm
Yes, it's work !!
I am going to test if the ref-seqs.qza and taxonomy.qza, which I have made, can make classifier successfully and work for my marker gene seqs analysis. And I will get back with if this trial have a new issue on the classification of marker gene..
May 8, 2022, 4:46am
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