assignments between snRNA and snATAC

[Parul-Kudtarkar]

We have snRNA & snATAC from pooled samples on which we ran vireo; is there a way to determine how consistent the assignments are btw RNA and ATAC?

Thanks you!

[huangyh09]

Hi, I suppose that you aim to compare the identified donors between RNA and ATAC, right? If so, you can compare the genotype returned from Vireo, e.g., follow this notebook: https://nbviewer.org/github/single-cell-genetics/vireo/blob/master/examples/donor_match.ipynb

Yuanhua

[Parul-Kudtarkar]

@huangyh09 thanks. Actually, thinking of (1) pool the cells per donor in ATAC and RNA, and then compare them to match up which is which, (2) go back to the original cells and see how consistent the assignments are per cell

[leeanapeters]

Hi, is there an easy way to do this when you have many wells? I have eight wells each scRNAseq and ATACseq of the same pooled donors (10x genomics) that I need to match. The notebook provides an example of just 2 samples but I will need to match within each modality and across the two.

Thanks

Leeana