Identifying appearance or disappearance of cell populations between WT and Mut single cell RNA-Seq data

Question

[AB]

Hi everyone,

I've done single cell RNA-seq data analysis using Seurat. Now if I have 2 samples, a wild type and a mutant and I want to find out if any new cell populations appear or any cell population disappears in the mutant, how do i test for it ?

I looked at this tutorial and it explains integration and finding differences in gene expression and identifying DEG across conditions, but not to check if there are any new populations appearing. What is the best way to do that ?

Answer 1

[igor]

You identify your clusters. Then you check the proportion of each sample within your clusters. It' unlikely that you will have a cluster completely unique to one sample. However, you may have a cluster that is, for example, 20% of one sample, but only 1% of the other sample. Thus, that population is enriched in the first sample.