This might be a very simple and a beginner question.
I have 6 10X scRNA_seq samples (control and treatment1) and have performed the QC and downstream analysis on them. We just sequenced 2 new single cell scRNAseq samples (10X chemistry) with different treatment (treatment2). Can I just perform QC on the new data and combine the Seurat objs of 6 and 2 samples and then perform clustering and if needed, perform batch effect or it is just impossible to even combine the two sets of data with different treatments?
Thank you very much!