And successfully obtained the resulting 'FeatureData[Sequence]' file.
Unfortunately I have no idea what to do next. None of the downstream steps in any of the tutorials I've seen take 'FeatureData[Sequence]' file types as an input from what I can tell. What is the next step here? My goal is to generate a feature table and proceed with the QIIME2 pipeline normally.
Sorry for the naive question, never worked with .fna files before.
I would recommend following the tutorial linked below - this will take you through the importing and de-replication process for .fna files, and will provide you with a feature table and associated feature data artifacts: https://docs.qiime2.org/2022.2/tutorials/otu-clustering/
In terms of what your next steps are after producing a feature table, that will be dependent on what the goal of your analysis is - QIIME 2 has many different plugins and tools available for microbiome analysis. I'd recommend looking over our available tutorials on the QIIME 2 Documentation pages - these will provide you with more details on the available pipelines within QIIME 2, and what the best analysis for your data is, depending on your study/goals/etc.
Hi @lizgehret , thank you for the reply! I've seen this tutorial as well, and when I run the dereplicate step I get the error:
(1/1) Invalid value for "--i-sequences": Expected an artifact of at least
type SampleData[Sequences] | SampleData[SequencesWithQuality] |
SampleData[JoinedSequencesWithQuality]. An artifact of type
FeatureData[Sequence] was provided.
Indeed, this is the error I get with any step I've ever tried - none of them seem to like the "FeatureData[Sequence]" artifact, although it was itself generated using QIIME2.