Extracting representative sequences from table


I have filtered my table.qza file containing all of my sequences based on those sequences found in a single sample using the qiime feature-table filter-samples command, but I was wondering if it was possible to extract those sequences as a rep-seqs file so that I can export it as a fasta file.

Any help would be greatly appreciated. Thank you!


Hi @bkramer,

I first want to note that my suggestion here is going to be making the assumption that you have a FeatureData[Sequence] artifact (which is very common - but please let me know if that is not the case, because this recommendation won't be possible without it).

With that being said, if you do have a FeatureData[Sequence] artifact with the "complete" set of features in it, then you can filter that file down using your filtered table. More information on this method can be found by entering qiime feature-table filter-seqs --help, just for your reference.

From here, you can use the output file from the above command (which will also be a FeatureData[Sequence] artifact) as the input for qiime tools export, which will allow you to export this data in FASTA format. More information on the parameters for this command can be found by entering qiime tools export --help, or checking out this tutorial.

Cheers :lizard:

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