I'm trying to understand the pipeline using PICRUSt2 to predict functional analysis on 16S data. As mentioned in this GitHub repository (PICRUSt2 Tutorial (v2.5.2) · picrust/picrust2 Wiki · GitHub), the tool requires three different input files.
My questions are: - Can I use the ASV file (denoised using DADA2) as input instead of OTU?
- 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?
- among the input files there is metadata.tsv but this file doesn't appear in the command lines as input
- 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?
- 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.
Yes, according to the tutorial, you can use either the ASV file or OTU.
This forum post describes how to convert .csv to a .biom table.
You are correct! it is not used directly in the commands. However, you may need it in your downstream analysis of the piecrust output.
Yes, you should be able to use that command.
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.
thank you for responding