How to generate a feature table from a .fna file?

Hi - I downloaded a publicly available dataset which is quite old, and came in the format as a single .fna file.

I imported it into QIIME2 using:

qiime tools import \
  --input-path sequences.fna \
  --output-path sequences.qza \
  --type 'FeatureData[Sequence]'

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.

Thank you!

Hi @mihcir,

Welcome back to the :qiime2: forum!

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:

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.

I hope this helps!

Cheers :lizard:

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.

Hi @mihcir,

My apologies, I should have been clearer when directing you to that tutorial - here's what you'll need to do in order to produce a feature table:

Starting from your .fna file, you'll want to follow this step in the tutorial to import it as SampleData[Sequences]:

qiime tools import \
  --input-path seqs.fna \
  --output-path seqs.qza \
  --type 'SampleData[Sequences]'

This will produce the required output for the subsequent command:

qiime vsearch dereplicate-sequences \
  --i-sequences seqs.qza \
  --o-dereplicated-table table.qza \
  --o-dereplicated-sequences rep-seqs.qza

From this command, you'll receive two outputs - one of which will be the associated feature table for your dataset.

Hope this helps!

Cheers :lizard:

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