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EDePasquale / DoubletDecon

A tool for removing doublets from single-cell RNA-seq data

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Running DoubletDecon on integrated seurat objects

saisomesh2594 opened this issue · comments

commented

Hello,

I was wondering if it is a good practice to run DoubletDecon on an integrated seurat object (multiple samples) or would you recommend to run DoubletDecon on seurat objects of individual samples and then remove putative doublets and then do the integration ?

Thanks,
Somesh

commented

Hello,

I was wondering if it is a good practice to run DoubletDecon on an integrated seurat object (multiple samples) or would you recommend to run DoubletDecon on seurat objects of individual samples and then remove putative doublets and then do the integration ?

Thanks,
Somesh

Hello,

The following link sheds some light:

satijalab/seurat#1814

I think it makes sense to run DoubletDecon on individual samples first and then try to integrate.

Best wishes,
Tushar

commented

Thank you for the question Somesh and thanks for the response Tushar, you are correct!

We suggest running any doublet removal tool, including DoubletDecon, on each sample first before integration.

Best,
Erica