I am about to filter and retain a lot of samples from feature-tables and them merge it in a merged-table.
These are soils samples, sequencing runs were done with the same primers/conditions and so DADA2 processing. The only difference is that data present in one of those tables was dereplicated with --p-maxee 0.5 while for the others I’ve set --p-maxee 2. However, I don’t see a problem here.
What I am thinking is the following: I am merging different feature-tables carrying different samples, however I am sure there are ASVs shared between those tables ( not sure how many) because many samples came from very close places. However, as they were processed independently, they’ll likely have different labels.
So, in the merging process, is there any “checking” for equal ASVs in terms of DNA sequence but with different labels? And if not, could someone provide me a hint on how to deal with it? I am affraid of ending up having unreal abundance and diversity results because of it.
I am considering align all the features I get from the merged-table and consider the ones with 100% Id as the same, but not sure if this is ok.
All the best,