How to reflect the table information, which singleton and non-bacterial OTUs are removed, at representative_sequence file.


Nice to meet you

While I study about microbiome analysis using qiime2, I have question at the step making phylogenetic tree.

After denoising step with DADA2 and Clustering, I got a table_clustered.qza file and representative_sequence_clustered.qza file.

Then, again, I modified table_clustered.qza file to remove singleton and non-bacterial OTUs. (final file name is table_clustered_singleton_non-bacterial.qza)

And I conducted making phylogenetic tree with representative_clustered.qza file without any modification.

Surely, that phylogenetic tree contains more amount of OTUs informations than modified table_clustered_singleton_non-bacterial.qza file.

Will that make trouble when I analyze beta-diversity (unifrac) with these two files?

If that is true, How can I reflect the table_clustered_singleton_non-bacterial.qza file OTU informations at representative_sequence.qza file.

Sincerely, I need your help.

Not at all. The UniFrac implementation in QIIME 2 will ignore any features that are present in the tree but missing in the table. So you do not need to re-make your tree.

Good luck!

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