I'm working on the ALS patients and comparing cases and control of this disorder. I already did single nucleus RNA sequencing for my controls (which were randomized with the samples from different region of case and controls of the same patients and some controls). Now, I would like to do the single cell RNA seq for my controls. But I'm worried that for downstream analysis it could be complicated as for batch correction. I really appreciate if anybody has any experience like this or any recommendation. I have the option to process one of the cases with these samples once more. I was wondering if it worth to do so.
I appreciate any comments