Correlation analysis in single-cell sequencing data

Question

[Yingying]

Hi everyone,

I am working with scRNA-seq and scATAC-seq datasets, and I'm wondering if it is suitable to apply correlation analysis to single-cell sequencing data given the sparsity of single-cell sequencing.

For example, I have two genes of interest A and B, one is upregulated and the other is downregulated in my cluster of interest. I would like to know how the expression of these two genes is correlated. However, in single-cell sequencing, most cells have zero counts for the genes, does a Spearman/Pearson correlation analysis still make sense in this case?

Thanks in advance!!