homotypic vs heterotypic multiplet output files

[AnjaliC4]

I have a very basic question about the outputs generated. Are both homotypic and heterotypic multiplets barcode ids in the MultipletCellIds_xx.txt ? If so, how can I find out from the output files of AMULET (without using the R vignette that you provided) which barcode ids are heterotypic vs homotypic?

Thanks again for this great tool for scATAC users! :)

Anjali

[alperoglu]

Hi Anjali,

Yes both the heterotypic and homotypic doublets are reported in the MultipletCellIds_xx.txt output file. These are not separated as homotypic and heterotypic, so you'll have to run the vignette for that.

However, you can also plot your cells on the UMAP dimensions with DimPlot function from Seurat and superimpose the doublet annotations. You can follow the end of our vignette here for that. We saw in our analysis that heterotypic doublets tended to form clusters on their own or be in-between singlet clusters like bridges. Homotypic doublets on the other hand tend to be found inside the singlet clusters. But I have to add that this does not give an official identification and that you have to run the R vignette for that.

Best,
Alper