Hi everybody,

We have scRNA seq data from 1200 cells from SMART-seq2 obtained from 3 runs:

• 1st run - 400 cells - 1st condition
• 2nd run - 400 cells - 2nd condition
• 3rd run - 200 cells 1st condition + 200 cells 2nd condition.

The cells from the 3rd run where already in the 1st or 2nd run.

Which controls do you think we have to check? Is it ok to start the analysis with all the data without merging runs? Normalization would do the work or do we need to run some previous steps? We are following the OSCA multi-sample tutorial from Bioconductor.

Many thanks for your help.