picrust2 input files ( for bacteria)

[jphagen (Johannah Hagen)]

Hi @Will_Ericksen,

@Will_Ericksen

• Can I use the ASV file (denoised using DADA2) as input instead of OTU?

Yes, according to the tutorial, you can use either the ASV file or OTU.

@Will_Ericksen

My ASV file is in .csv format. How can I convert it to a table.biom format or I just converted to .tsv and run the script?

This forum post describes how to convert .csv to a .biom table.

@Will_Ericksen

among the input files there is metadata.tsv but this file doesn't appear in the command lines as input

You are correct! it is not used directly in the commands. However, you may need it in your downstream analysis of the piecrust output.

@Will_Ericksen

Can I install PICRUSt2 using this command: conda create -n picrust2 -c bioconda -c conda-forge picrust2=2.5.2 instead of mamba create -n picrust2 -c bioconda -c conda-forge picrust2=2.5.2 because I don't have Mamba on my Linux?

Yes, you should be able to use that command.

@Will_Ericksen

Does the installation of PICRUSt2 using Conda take too much time? The environment solving process has been running for 2 hours, and the package is not yet installed.

If the installation is taking too much time you may want to install mamba to make the process more efficient.
There is also this option available to you. Which avoids a mamba install, but will need to be run within a qiime2 environment.

I hope this information is helpful to you! Feel free to reach out again if you have more questions.

-Hannah