I have a snRNA-seq dataset with 6 samples with 12 runs(2 different tissues coming from 6 individuals).

I want to compare expression profiles between tissues for each individual separately and then integrate them all together for combined analysis. While for integration there are programs like Harmony which will let me do that. But for individual analysis I have used Kallisto-bustools for matrix generation and I have a matrix for Frontal and Motor cortex separately and programs like Deseq2, MAST need a single matrix as input.

1. Can I simply concatenate the matrix while minding the gene arrangement for differential gene expression and do other comparisons like cluster analysis and cell annotation with separate matrices?
2. Is matrix concatenation better for all of downstream analysis?
3. Is there any differential gene expression analysis program that take two matrix as input?

Thanks for your time, sorry if the question is weird.