Filter ATAC before running scDblFinder

[plger]

Filter ATAC before running scDblFinder

[plger]

Hi,

Actually it turns out that scDblFinder and its thresholding procedure are pretty robust to prior filtering or not, so I don't think the results will change much (unless you're filtering out a majority of cells).
The same therefore applies for ATAC-seq when using the aggregation-based method.

Regarding the Amulet method, it's anyway is largely independent across cells and hence of prior filtering (the only impact across cells is the filtering out of possible repeat regions).

So in conclusion: it shouldn't make much of a difference.

[ccruizm]

Thanks for the speedy reply and for clarifying this! It is good to know that it won't impact the performance of the doublet calling.