Merge or discard sequences from duplicated samples across multiple runs?

[Mehrbod_Estaki]

Hi @groot,
Welcome to the forum!

@groot

what should I do with these duplicated samples moving forward?

I would drop the one with the least sequences. Manually go through the separate runs and use filter-samples to remove those.

@groot

is there a generally accepted threshold for the minimum number of sequences that a sample should have?

Not really, it really depends on your sample type and what kind of biological question you are trying to answer. See this thread for a little more in depth answer

I wouldn't merge the 2 samples, the risk of combining batch effects from 2 separate runs is too great. This will likely lead to these merged samples to have an artificially unique signature resulting from the merging that other samples didn't have.