I have a question about filtering features that I have been unable to find a solution for. I have datasets with two and three different samples collected from the same individual, and approximately 100 individuals. I wish to identify and keep only those ASVs found in sample A, but not in sample B (and C) for each individual. So for individual1 I wish to find all ASVs with sequence count 0 in B and >0 in A… Does anyone know a solution for this?
I think there is a way you can do this using the examples in the filtering documentation.
The idea would be to
qiime feature-table filter-samples to divide your table into separate cohorts, filter to only get features >0 in each cohort, then get those feature IDs. That would give you
With those lists, you can filter the other cohorts to just include these features.
You could also approach this question from a different angle.
Instead, you could identify ASVs differentially expressed in sample A compared to B and C using a plugin like ALDEx. Your initial question asks only about presence or absence, but change in amount could be interesting too!