q2-sapienns: total sum scaling

Community Plugin Support
1

Hello!

I have a taxonomy table from MetaPhlAn4, and I used q2-sapienns to create a feature table (relative frequency) that I can use in QIIME2 for analysis. I want to work with count data, and multiply all the relative abundances by a constant (ex: 100,000), ie total sum scaling. Is there a way to do this within the q2-sapienns plugin, or another QIIME2 plugin?

If I do total sums scaling directly to the mpa4 taxonomy file, it cannot be uploaded via q2-sapienns because it's not in the correct format.

Thanks for your help!

3

Hi @em_joyce,
You can do this using qiime sapienns frequency --p-target-freq 100000.

And I just want to point out this note from the q2-sapienns README.md file:

q2-sapienns is comprehensively unit tested, but hasn't been field-tested much yet. If you notice any issues, please post to the issue tracker.

Good luck!

Greg

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