A couple of members of my lab and I have been getting very different results when using qiime2 versus phyloseq for calculating weighted unifrac values. It seems that the default parameters used by these tools (qiime diversity core-metrics-phylogenetic versus phyloseq::distance) generate very differe…

Thanks for the notebook, that is wonderful! I haven't looked too closely yet, but it is it possible that we're just seeing the result of rarefying twice? Granted I wouldn't expect weighted unifrac to look that different between different rarefactions, but that's the most obvious place to look initia…

I'm confused by "rarefying twice". If the rarefying depth for qiime diversity core-metrics-phylogenetic is set to the same value as the table that's already rarefied, shouldn't that essentially be the original counts? Rarefying in qiime2 by default is without replacement, correct?

Yeah, at least for qiime feature-table rarefy, the docs state: Subsample frequencies from all samples without replacement so that the sum of frequencies in each sample is equal to sampling-depth. So, rarefying a table that's already been rarefied to that depth shouldn't change anything, correct? …

[image] nick-youngblut: I’m confused by “rarefying twice”. If the rarefying depth for qiime diversity core-metrics-phylogenetic is set to the same value as the table that’s already rarefied, shouldn’t that essentially be the original counts? Rarefying in qiime2 by default is without replacement,…

No worries! I'm worried about the differences between phyloseq and qiime2, at least for their defaults. Both methods are used by members of my lab, so they may be getting very different results just because they are using phyloseq versus qiime2

[image] nick-youngblut: I’m worried about the differences between phyloseq and qiime2, at least for their defaults. Of course! Pinging @wasade who's implemented a whole slew of UniFrac varieties. Any idea what variety of UniFrac Phyloseq might be using here?

@wasade @ebolyen @nick-youngblut linking to the phyloseq source code for convenience: joey711/phyloseq/blob/master/R/distance-methods.R#L565 # Fast UniFrac for R. # Adapted from The ISME Journal (2010) 4, 17-27; doi:10.1038/ismej.2009.97; # http:/…

@nick-youngblut , I’m not sure of the source of the difference but thank you for flagging it. Weighted UniFrac is deterministic, and the implementations of UniFrac used by QIIME 2 are validated against the original implementation of UniFrac by Cathy Lozupone from PyCogent (unit tests for the version …

I posted an issue on the phyloseq github site the same day that I posted to this forum.

Great, thank you for doing so. Best, Daniel

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Very different weighted unifrac results for qiime2 versus phyloseq

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