Kind of just a conceptional/workflow question regarding filtering specific taxa - why would one prefer to filter sequences over filtering a table or vice versa?
Would filtering a table be more desired if you were analyzing different subsets of the same data and filtering different taxa? Not sure why you would do that, but was the only thing I could think of…
The two options you mentioned, filtering features & filtering sequences, are meant to give one the flexibility of manipulating their data to match what they need for their analyses. There are many different reasons why the two are helpful. Here’s just a small example:
I run an animal experiment and collect fecal samples from pre and post treatment, but I also collect colon tissues at the end. I extract DNA, and prepare my amplicons for the fecal samples on a separate day than the colon tissues. I sequences all my samples in one run and now I want to play around with the data.
Right off the bat, I am interested in looking at fecal samples separately because for this analysis I can do a longitudinal analysis of pre-and post. I use the filter-samples option to create a subset of my data that contains only the fecal-samples. I do the same on a subset of colon-tissues to analyse separately.
While I’m analyzing the colon-samples I notice that there is an usual bacteria in all the samples that is commonly not found in mouse tissue. I later find out that perhaps that is a result of some cross-contamination from another study happening in the lab which was culturing that specific bacteria. Instead of tossing away my whole data, I can now go ahead and remove that bacteria from all my samples as I know it is contamination. Or perhaps you also want to remove all features that hit as Chloroplast and Mitochondria from your table. There are of course lots of other examples that you can do with these options, limited to your imagination and need.
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