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plger / scDblFinder

Methods for detecting doublets in single-cell sequencing data
https://plger.github.io/scDblFinder/
GNU General Public License v3.0
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Filter ATAC before running scDblFinder #76

Closed ccruizm closed 1 year ago

ccruizm commented 1 year ago

Good day,

I wanna use scDblFinder on my scATAC data. For RNA, you warn users to perform initial QC so it does not influence the modeling of doublets for more precise doublet calling.

I have checked the ATAC vignette but could not find information about this particular point. What would you recommend?

I appreciate any suggestions you can give me.

plger commented 1 year ago

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 commented 1 year ago

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.