Adding new samples to single cell rna-seq analysis

Question

[maria2019]

Hi,

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?

Answer 1

[heskett]

luckily the CellRanger software has built-in programs to do exactly this. check out the aggregate function as a starting point

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ag

[maria2019]

Thank you very much!