Convert qza to txt or FASTA or biom

Hi everyone,

I need to convert the output of “qiime feature-classifier fit-classifier-naive-bayes” to FASTA file.
I have already tried using “qiime tools export” command, but it did not give to me a BIOM file; the output was a PKL file, which I could not open nor convert into txt file.

How can I get a FASTA/txt/biom file from my qza table?

Thank you for your help.
Best regards.

Charlotte

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fit-classifier-naive-bayes produces a trained classifier, not a fasta file. This trained classifier is not really meant to be human readable so there is not really a reason to export this, and there is certainly no way to get a fasta file from that.

The only FASTA you can get out of this process is by exporting the reference sequences that are used to train that classifier, or by exporting your query sequences.

What are you trying to do? What are you hoping this FASTA would contain? If you can give me more details on why you hope to accomplish, I can point you in the right direction.

Thank you Nicholas,

I am trying to use the trimmed reference greengenes sequences to use them in another programme; currently, I am working with reads from Nanopore MinION.
Anyway, if it is not possible to convert the output.qza to fasta file, maybe it is better to import the demultiplexed fasta file from MinION into QIIME and then directly run the “qiime feature-classifier classify-sklearn” in order to classify the sequences?
is that a good option considering the high error rate from Nanopore reads?

Thank you a lot!!!
Best regards.

Charlotte

You can collect the reference sequences here, trim using extract-reads, and then export to fasta.

The trained classifier does not contain the actual sequences, though.

That’s certainly an option — it is worth trying. I have not tested accuracy with nanopore reads so cannot speak to how the error rate will impact accuracy.

One thing to keep in mind: if the nanopore reads are in mixed orientations (i.e., not all reads go from forward to reverse primer in the same direction), it can cause problems with classify-sklearn. classify-consensus-blast and classify-consensus-vsearch will not have that problem.

I hope that helps!

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