Hi, I would like to import and analyze a data set that is in QIITA and has a deblur .biom table generated. Importing the .biom table seems straight forward, but I am unsure how to generate the rep-seqs.qza file needed for taxonomic classification. I have the full seqs.fna file from QIITA. Thanks!
Hi @jessicalmetcalf! You can use the new q2-vsearch method dereplicate-sequences to convert your seqs.fna file to a FeatureTable[Frequency] and FeatureData[Sequence]! Check out @gregcaporaso’s draft community tutorial on q2-vsearch, in particular, the section titled “Dereplicating a SampleData[Sequences] artifact.”
Once you have those two new artifacts, you could either perform OTU clustering (see the rest of that draft tutorial), or continue on with generating summaries.
Hope that helps!
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Hey @jessicalmetcalf, are you referring to reference-hit.seqs.fa? If so, that file has a one-to-one relationship to the features present in reference-hit.biom, and you should be able to bypass the vsearch step and go straight to qiime tools import --input-path reference-hit.seqs.fa --output-path rep-seqs.qza --type FeatureData[Sequence]. If don’t have reference-hit.seqs.fa, you can download that file from Qiita on the same page where the reference-hit.biom was obtained.
Best,
Daniel
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