Selection (or deletion) of some samples from the qza files of table and rep-seqs?


I have analyzed the seqs from 61 samples, using table.qza and rep-seqs.qza from dada2 step. Now I would like to analyze them from some selected samples for making different types of data (e.g., PCoA for differently selected samples).

Q: is there any way to analyze the seqs from selected samples using the previously obtained table.qza and rep-seqs.qza? It would be great if I could select or delete the wanting sample data from those files and use them for further qiime analyses.

Thanks for your cooperatives,


Hi @baehsung,
there are many ways to filter your table.qza to keep or exclude one or more samples.
Please see the tutorial 'Filtering data — QIIME 2 2023.5.1 documentation'

Look at 'Identifier-based filtering' section for clarification as one possible way.

Once you have the table.qza including only the samples you would like to analyze, that will be enough. Most of the analyses select only the sequences for the ASVs in samples form the ASV table you are using, if the sequences are necessary.

Hope it helps

Thanks Luca,

I'll look at the tutorial and get back for further discussion.


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