Filtered data from cellranger

[silvainp]

Hi everyone,

thanks for this very straightforward package. Short question, do you think that the quality of the filtration by cell ranger matters in the SoupX output?

My point is, we have a 10x dataset showing 30k cells in the filtered, even if we know only 10k are proper cell. Is feeding SoupX with this fille will underestimate the soup and make it less efficient? And if so, should we give it an own version of the filtered dataset containing 10k cells?
Many thanks for your input.

SiP