I need a FeatureData[Sequence] for the open-reference vsearch function, but I cannot find a way to create one. I am starting with SampleData[PairedEndSequencesWithQuality], and running "cutadapt trim-paired" and "dada2 denoise-paired". Out of the 3 input files I need, dada2 provides 2 of them.
dada2 outputs FeatureTable[Frequency] and FeatureData[Sequence] artifacts that you can use as input to the OTU picking method.
Sounds like you are confused about where the second FeatureData[Sequence] artifact, "reference-sequences", comes from. This will be the reference sequences you wish to use, e.g., from SILVA or greengenes, imported as a FeatureData[Sequence] artifact.
Good luck!
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