Import representative sequences from txt file

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I have a .txt feature table which includes a column of 16S sequences for ASVs. I am not sure how to import these as a representative sequences .qza object. Any advice is appreciated!

2

Hi @naomig ,

It sounds like you have your data in an unusual format. To import the representative sequences as a FeatureData[Sequence] artifact, you will need to:

  1. extract only the column containing sequences (outside of QIIME 2)
  2. convert this to FASTA format somehow (outside of QIIME 2)
  3. import following these instructions: Importing data — QIIME 2 2022.11.1 documentation

Steps 1-2 could maybe be done with biom-format, but I am not sure.

Whoever gave you the TXT table might also have the sequences in FASTA format somewhere... I would start there if possible.

Good luck!

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Thanks! I ended up converting to FASTA format in Excel (by adding ">Seq[ID]" in a row above each sequence) and saving as a txt file, which QIIME was able to read.

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