Hi everyone!
I want to collapse my sequences to genre level in order to generate a phylogenetic tree. I know how to do this to the frecuency table with qiime taxa collapse So I thought I could filter the sequences with qiime feature-table filter-seqs but It seems like I can’t (All features were filtered out of the data.).
I also know that I can try with phyloseq R package, but I wanted to ask If there’s a way to do this in qiime2.
Hi @jose_gacia,
That is because when you collapse based on taxonomy the feature IDs become the taxonomic lineages and no longer correspond to your sequence IDs.
When you collapse on taxonomy there is no single sequence that represents the clade. I am not sure what phyloseq does but there is not an equivalent in QIIME 2 for selecting a single representative sequence from within a group of ASVs that share the same taxonomic lineage.
Good luck!
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