How do I create a taxonomy file

Hi,

I was just wondering how do I create a taxonomy file using QIIME2? In the moving pictures tutorial, I’ve reached the Taxonomic analysis but I realised I need a feature classifier? How do I choose what is my feature classifier? Any help would be much appreciated. Thank you.

Hi @Jan,
If you are following the moving pictures tutorial, pay close attention to the “Blue boxes” sometimes they contain really important information that users overlook some times.

So under the Taxonomic analysis section it points you to the tutorial that covers this topic comprehensively about how to train your own. Can you give that a try and then let us know if you still have any questions.

Note

Taxonomic classifiers perform best when they are trained based on your specific sample preparation and sequencing parameters, including the primers that were used for amplification and the length of your sequence reads. Therefore in general you should follow the instructions in Training feature classifiers with q2-feature-classifier to train your own taxonomic classifiers. We provide some common classifiers on our data resources page, including Silva-based 16S classifiers, though in the future we may stop providing these in favor of having users train their own classifiers which will be most relevant to their sequence data.

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Hi @Mehrbod_Estaki,

I’ve been advised to used BLAST+ method for taxonomy classification with GreenGenes (GG) database at 99% sequence similarity. However, when trying to input the data, I received this error message, do you know what this means and how do I solve this?

Hi @Jan!

I don’t see an error message here, just output logs letting you know that the command is running (and so far, it all looks successful!). If you’re observing an error, please copy-and-paste the complete output from the command - thanks!

:qiime2:

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An off-topic reply has been split into a new topic: How do I convert my rep-seqs.qzv file to a biom file to visualise the OTU-sample relationship?

Please keep replies on-topic in the future.