Hi everyone,

From 3 donors, I isolated 2 cell populations (Xneg and Xpos) from blood and tissue. They are then sequenced separately, giving me 4 10X Cell Ranger datasets (matrix.mtx, genes.tsv, and barcodes.tsv):

I hope to combine datasets 1 and 2 to perform two pooled analyses (clustering and DEG) for:

• All 3 donors together
• Each donor separately

I will do the same for tissue datasets 3 and 4.

Finally, I hope to compare the analyses between blood (1 + 2) and tissue (3 + 4).

Would anyone mind suggesting the best ways to go about doing these? I looked through previous issues on integration and vignettes on Seurat website, but I am still a little confused of which functions and workflows to follow.

Any pointers for strategy, functions, packages, or tutorials would be greatly appreciated. Thank you very much!