Does vireo catch both hetero- and homo-zygous doublets?

single-cell-genetics / vireo

Demultiplexing pooled scRNA-seq data with or without genotype reference

https://vireoSNP.readthedocs.io

Apache License 2.0

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Does vireo catch both hetero- and homo-zygous doublets? #79

Closed ollieeknight closed 1 year ago

ollieeknight commented 1 year ago

Or just heterozygous, due to different SNVs at the same site. Furthermore, does the presence of cycling cells (with more than two copies of each DNA strand) affect deconvolution? I know that for example AMULET (https://github.com/UcarLab/AMULET) has this problem.

ollieeknight commented 1 year ago

I mention this, because I have a hashtagged multiome dataset where, without removing hashtag doublets (but removing unassigned and vireo doublets, the hashtag-by-hashtag plot looks like...