Hi, I am new to QIIME2 and currently using v2023.2 in a conda environment. I am doing 16S analysis and planning to combine samples from two different runs to increase my sample size (Examples: Samples 1-5 are on run 1 and samples 6-10 are on run 2).
I have already denoised the two runs separately based on dada2. I am referring to the Fecal Microbiota Transplant Study for combining the two runs. I have three questions:
While using the feature-table summarize command (below), we need to enter the sample metadata. Do I need to create a new metadata file combining the two runs?
If I need to choose to analyze only certain samples for a given analysis. Let's say samples 3 and 5 from run 1 and samples 7 and 8 from run 2. What is the best way to do that? Should I just edit the metadata file and remove everything except those samples?
Thank you and appreciate everyone's help in my QIIME2 learning thus far!
Yes, just concat or merge both metadata files to create a new one for merged tables.
Just remove undesired samples from metadata file and then filter feature table based on sample IDs in metadata file, like in this tutorial. BTW, check this tutorial, it contain a lot of examples how to filter your data based on features, samples, metadata columns and other parameters!