In the DADA2 table file, instead of the feature id we would like to have the taxon_id as shown in the visual taxonomy file. Is there a Qiime command to do so?
For example we would like to change the following
d__Bacteria; p__Firmicutes; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; g__Howardella
The result would be a DADA2 table or .qza object with the taxononmy information instead of the ID
Hi @shuanqiime, welcome to !
The best way to do this would be to run:
qiime taxa collapse \
--i-table feature-table.qza \
--i-taxonomy taxonomy.qza \
--p-level 7 \
Keep in mind that you can have many features with identical taxonomy assignments. So, this command will essentially merge together all features sharing the same taxonomy together as one unit. The values in the table will be the sum of all those individual features that were combined under that taxonomy.
That was great! Thanks so much. Your solution worked.