Is there any way to analyze the microbiome functionality with QIIME2.
I have the following files:
- the forward reads (****_L001_R1_001.fastq.gz)
- the reverse reads (****_L001_R2_001.fastq.gz)
And I have already imported my data into QIIME2 and got the *.qza file.
I performed the sequence quality control and feature table construction, FeatureTable and FeatureData summaries, generated the tree for phylogenetic diversity analyses and the alpha and beta diversity analysis.
What I want to know is if I can perform something like this:
Thanks in advance.
As I understood, you have 16S amplicons that you successfully analysed in Qiime2. Unfortunately, from this type of data one can not obtain actual functional annotations, since for it shotgun data is needed. However, one also can get functional predictions (functions are predicted based on 16S data). This analysis can provide some insights, but it is not actual observations.
Here is a link to q2-picrust plugin to get functional predictions.
Thank you so much for your response.
That is exactly what I need. I need to get functional predictions out of my 16S amplicons. I tried to install the q2-picrust plugin but I am getting the following error message: "mach-o file, but is an incompatible architecture (have (arm64), need (x86_64) " I guess I have to wait for an update. I've noticed that it has not been updated since 2021. Hopefully they consider upgrading it.
Thank you so much!
While waiting for an update (I don't know if or when it will be), you can install and older version of qiime2 (no need to uninstall newer qiime2) and install plugin there. Or you can use standalone version of picrust2, but you will need to export q2 files into compatible format.