About qiime metadata tabulate

[F18D029G (Kohei Takahashi)]

Hello

I use follow command.

qiime metadata tabulate
--m-input-file rep-seqs.qza
--m-input-file taxonomy.qza
--o-visualization tabulated-feature-metadata.qzv

The contents of tabulated-feature-metadata.qzv are shown below.

All are assigned to Glomus, but some have low "Confidence".

Is the "Confidence" value of this assignment worthy of trust?

Thank you
Kohei

[Nicholas_Bokulich]

@F18D029G

Is the “Confidence” value of this assignment worthy of trust?

You can adjust the confidence threshold for classification. The default settings have been benchmarked for optimal performance.

However, those confidence values probably are not trustworthy. If every single classification is "Glomus", I suspect something is wrong with your classifier. Did you use extract-reads on the reference sequences by any chance? See this topic — and note that extract-reads has a min-length parameter to fix that issue in the latest release of QIIME 2.

[F18D029G (Kohei Takahashi)]

Thank you for your reply!!

How is the default confidence threshold setting?
I don’t know how to change confidence threshold.

I didn’t use extract-reads.
Is extract-reads the procedure necessary for the analysis of qiime2?

Thanks
Kohei

[Nicholas_Bokulich]

@F18D029G

How is the default confidence threshold setting?
I don’t know how to change confidence threshold.

You can change the confidence setting in classify-sklearn

@F18D029G

I didn’t use extract-reads.

Oh. Then maybe I misunderstood your question and this is not a problem at all. What reference database did you use?

@F18D029G

Is extract-reads the procedure necessary for the analysis of qiime2?

Not at all! And in fact I discourage it with the UNITE fungal ITS database (which is what I assume you used).

[F18D029G (Kohei Takahashi)]

Thank you, I will check classify-sklearn parameters.
How much confidence threshold setting is trustworthy?

I used MaarjAM database.
MaarjAM database contain only Glomeromycota sequence.

Thanks
Kohei