I've run a group of samples from 7 different locations. I've already got these results (alpha, beta-diversity and PCA). Now, I want to reanalyse a subgroup of these samples (just want the samples from two locations).
When Im running the commands for getting statistics graphics, the .qza that I need as inputs are: repseqs, table and filtered table.qza. Is there any way I can eliminate from table.qza all the samples that i dont want to include so I can use it for repeating the commands from this point till having the new filtered_table.qza and use these 3 .qza for getting the statistics graphics?
Great question - what I'd recommend doing is running filter-samples using the --p-where parameter on your location column within your metadata file. You can then just re-run core metrics (assuming you are wanting to perform the same analyses on this subgroup - alpha/beta div, etc) using your rep seqs file and filtered table. You don't need to worry about filtering your rep seqs file as it will only pull samples that are in your rep seqs as well as your filtered table.