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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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Using both scATAC and scGEX combined from 10x Multiome for doublet calling #43

Closed eliascrapa closed 3 years ago

eliascrapa commented 3 years ago

Hi,

I have 10X Multiome data where we have scATAC and scGEX data from the same nucleus. As is understand scDblFinder can use either ATAC or Genexression data to call doublets. Would it be possible to use both assays together for doublet-calling?

Thanks

plger commented 3 years ago

Hi, at the moment, no. You can call doublets on both modalities (on ATAC using the procedure described in the latest vignette) and compare the scores, for instance do a weighted average. But right now it can't be done together with a single model. We're trying to check to what extent this is worth doing (i.e. how much it brings), and if we see that it does we'll implement it, but in the absence of multiome data with ground truth doublets (e.g. SNP-based), that's a bit tricky. If you know of such data, let me know :)

eliascrapa commented 3 years ago

Thanks. Sorry for the lack of an answer. I am looking forward to your implementation. Meanwhile i will go with the RNA data part.