Demultiplex droplet single-cell RNA-seq data based on sex

Question

[ic23oluk]

Hi,

There's a bunch of tools exploiting SNPs to demultiplex scRNAseq data, i.e.:

1. Vireo
2. demuxlet
3. fremuxlet
4. scSplit
5. Souporcell

My Question is, do these tools work when pooling genetically identical samples, but of different sex (so actually not genetically identical), by means of the y-chromosome?

Thank you.

[ATpoint]

Wouldn't it be much simpler to run a PCA only on chrY genes and see whether there is any separation? That should be rather bimodally clear, I would think.

[ic23oluk]

That does indeed sound a lot simpler. In that case, I would run the standard Cellranger pipeline and then in for example seurat run PCA on y genes and assign genotypes, right?

[ATpoint]

I would at least try that first. Cannot tell whether it works but chrY genes should have mostly zero counts in females so I'd be surprised if PCA would not be able to separate the sexes in the early PCs.

[garyhokawai]

Actually this doesn't work. There are over 700 genes in mouse chrY, but only a few are expressed or captured by single-cell RNA-seq. And there are negative expressions of these sex-specific genes. One example is Xist in female samples, the positivity of XIst never get to 100% in single-cell data.