Dear QIIME2 users
When I used the SILVA_132_QIIME_release database to classify, I got some taxonomic status named “metagenome”.I didn’t know what should I do about this.
On the one hand, there are no one by the name of “metagenome” in systematics.On the other hand ,it is a real classification come from Silva database.
What should I do? Can I just remove the classification, or rename them to uncultured bacterium or unclassfied bacterium?
Thanks in advance for the help.
Last time I was working with Silva, I went through and reclassified those as “unspecified genus X” (and similiar) using a custom python script. (Missing levels ended up as unclassified.) It’s ugly, but it worked?
Hi! I encountered them as well. Left them without changes for now since they are not significant in my data. But found some errors in Silva 132 database beside it.
Thanks for your reply!
I will try to use your python script to clean silva taxonomy.
As others already mentioned, I customized those undefined taxa in my Silva in a way that “metagenome, environmental…” and others came to “unclassified_X” and that’s how I deal with them.
All the best,
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