Could anyone please let me know how to produce the taxonomy.qza file to be at genus taxonomy rank only not to species?, I'm not talking here about the feature table that can be collapsed to the interested taxonomy rank.
is there any command to perform this filtration with qiime2?
Thanks in advanced
Hi @Za85, welcome to !
What are you trying to accomplish?
You can either filter by taxonomy to remove anything that does not have at least a genus label.
You can also, install the RESCRIPt plugin, and then run qiime rescript edit-taxonomy ..., to remove parts of the taxonomy after any rank you wish.
You could also combine both of these steps.
I'm grateful for your reply and suggestions,
from the tutorial of RESCRIPt;
''You can also choose the taxonomic ranks you'd like to backfill using the
--p-rank-handles flag. Which we won't set here, as the default, e.g. :
`--p-rank-handles 'domain' 'phylum' 'class' 'order' 'family' 'genus' 'species''
This is what I'm looking for, so I'll follow this tutorial.
thank you again
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