I am a bit confused about the unassigned taxonomy using QIIME2.

Using QIIME2 we can get the microbial taxonomy along with the Unassigned taxa written as "Unassigned". Besides that, we also get different signs such as;, , p;, g;_. Should I consider these unassigned or exclude it? if these are unassigned taxa then why these are not included in the word "Unassigned". Recently, one of the reviewers asked about the large proportion of unassigned reads in our study. We always consider or count all these signs (;, , p;, g;_.) as Unassigned that might be the reason for having a large proportion of unassigned taxa reads. We are using both silva and greengene databases. Kindly help me in this regard. Thanks

Could anyone please help me in this regard?

Hi @hussain
Please, be patient and read the Code of Conduct.
One of the moderators already assigned your topic to himself and will give you an answer shortly (most of the moderators are Qiime2 developers and answering questions in their free time).


Hi @hussain,

Thanks for your patience! I will follow up with you on this first thing Monday morning. Hope you have a great weekend! :slight_smile:

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Hi @hussain, thanks again for your patience here! A couple of recommendations below.

Rather than unassigned, these are actually unidentified taxa. You'll see this syntax whenever there is information at that taxonomic level, but the current database being used wasn't able to identify it. I would highly recommend retaining these samples, since they are valid data that just hasn't been identified in either Greengenes or Silva thus far.

It may be helpful to count these in a new category that you have labeled as unidentified (rather than unassigned), just for accuracy's sake - but that is ultimately up to you and your team.

Hopefully this helps!


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thank you so much for making my concept more clear. Definitely, we will consider your kind recommendations. Thanks again.

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