Need help separating fetal from maternal cells in placenta

[bkheira]

Hello,

I have a single cell dataset with immune cells sorted from placentas. Recently I found out that the immune cells could be either fetal or maternal, even at the beggining of the gestation. Since that, I have been trying to use Souporcell to separate these two origins of cells.

I have been using the regular pipeline indicating the bam file, the reference genome, and the number of clusters expected (2). It always gave me about half of fetal and half of maternal cells, which is surprising biologically. I tried souporcell with another dataset of placentas where I know which cells are maternal and which cells are fetal (about 10%) and it still gives me 2 clusters with around 50% of each type.

I think I have been doing something wrong and would like to know how you used souporcell in your publication to separate the two cell populations. Could you please help me and share your computational method for that ?

Best, Kheira