Adding new samples to single cell rna-seq analysis
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?
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