I am looking for some additional resources or suggestions to help me get started using PICRUSt2. I am using the qiime2 plugin for PICRUSt2 (installed as directed here: q2 picrust2 Tutorial · picrust/picrust2 Wiki · GitHub) and have been through the brief mammalian stool tutorial successfully. I’ve also read through the picrust wiki and tutorials.
I have ~300 human gut microbiome samples and have previously followed a filtering/processing/diversity analysis workflow using phyloseq and MaAsLin2. (An outside lab ran the 16S sequencing and taxonomic classification using qiime2/dada2 and provided me with the files.)
I have a few questions for getting started with running the q2-PICRUSt2 pipeline:
- Should I start with the original data (the .qza files) provided to me or the filtered data? I ask because I did some taxonomic/prevalence filtering in phyloseq; thus the number of taxa in my samples is different in my post-phyloseq workflow. Would this impact my PICRUSt results? Based on the information in the PICRUSt2 tutorial, it seems like I would be OK to use the filtered data. (PICRUSt2 Tutorial (v2.3.0 beta) · picrust/picrust2 Wiki · GitHub)
- If the answer to #1 is that it is OK to use my post-phyloseq data, what is the best way to export the phyloseq object into PICRUSt?
I’m pretty new to qiime2/picrust/etc, so thanks for any advice.