Entering edit mode
3.2 years ago
paria
▴
90
Hi everyone,
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
Out of curiosity why are you performing both snRNA-seq and scRNA-seq on your control samples?
Sorry, I meant sn-RNA sequencing by single cell. I did just sn-RNA seq.
Integration of datasets generally mitigates many of the effects of batch in standard single-cell analysis. See chapters 13 (and additionally 7) in OSCA, or the Seurat integration vignette.