Rarefaction after collapsing to genus level

Hello and thanks for this great community!

I am using qiime2 and r for my analysis.
After dublur I usually export the feature table and taxonomy to r, then for alpha and beta diversity I do rarefaction with phyloseq.
Usually, for differential abundance analysis, I use the raw biom table and collapse to genus level.
Today I was asked to generate a rarefied table at the genus level. If I’m doing rarefaction of the feature table and then collapsing to genus - I get very different row sums for each sample.
Is it possible that I am losing genera that were unclassified to the genus level?

Thank you,

Hello Lena,

It is possible, as phyloseq handels missing taxa differently depending on how they are represented in the tax table (NA vs g__).

Can you post the phyloseq code you are using to rarefy and tax_glom, along with the resulting counts? Thanks!

P.S. I've moved this to 'Other Bioinformatics Tools' as I think this is more of a Phyloseq question.

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