# Which files to use in q2-picrust2 pipeline?

**URL:** https://forum.qiime2.org/t/which-files-to-use-in-q2-picrust2-pipeline/19216
**Category:** PICRUSt2
**Tags:** picrust
**Created:** [April 14, 2021, 8:02pm UTC](https://forum.qiime2.org/t/which-files-to-use-in-q2-picrust2-pipeline/19216 "2021-04-14T20:02:52Z")
**Posts on this page:** 1
**Showing post:** 5

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### Author: ![basil0125](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/b/c67d28/32.png) [@basil0125](https://forum.qiime2.org/u/basil0125)
#### Post date: [May 10, 2021, 4:19am UTC](https://forum.qiime2.org/t/which-files-to-use-in-q2-picrust2-pipeline/19216/5 "2021-05-10T04:19:24Z")

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Hi-

Thanks for your responses! I ultimately decided to use the original files from QIIME2 and the re-process them in the same way that I had it in phyloseq. (I also managed to export the phyloseq OTU table to a .biom format using this information: [Importing dada2 and Phyloseq objects to QIIME 2 - #4 by ChristianEdwardson](https://forum.qiime2.org/t/importing-dada2-and-phyloseq-objects-to-qiime-2/4683/4)).

> I’m wondering where you are getting this estimate?

The [tutorial](https://github.com/picrust/picrust2/wiki/q2-picrust2-Tutorial) says that the full PICRUSt2 pipeline takes about "~15 min and 3.8 GB of RAM". Perhaps this is just for the mammal data. Mine took about an hour, even though I allocated 10GB to the virtual box- could just be that my computer is slow, or that I have more samples.

Any suggestions for additional downstream tools? I imported my pathways & ko back into R to do some ordination and PERMANOVA testing. I also read that some people like to use the STAMP software, but I've also seen some instances of differential abundance testing for the metagenomes and pathways. However, I haven't been able to figure out if this is kosher or not.

Thanks again.

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