When to merge scRNA datasets

Question

[bioinformatics.girl]

Hello-- I am running an scRNA-seq analysis against 10 different generated datasets. They are either separated into FLOX or KNOCKOUT. Do you analyze each dataset separately, or do you merge the 5 FLOX together and separately merge the 5 KNOCKOUT datasets *and then analyze the assumed 2 datasets instead of 10?

Could you explain this more. Thank you!

[jv]

What do you mean when you say "merge"? Are you referring to integration of the data sets? Are the 5 FLOX samples replicates?

[bioinformatics.girl]

Figure it out. thanks