I have 3 fish groups differently treated. With scRNA-seq and data analysis using Seurat, I found out there a big variation in the cell numbers/treatment. Given that the batch effect was controlled, and this variation is demonstrating the same pattern across all the replicates, what sort of analysis in Seurat can support or refute that this finding is attributed to the different treatments?
I mean the actual cell numbers found in each sample, and the cells are in vivo treated. That's right, a technical variation or other accidental error might have happened. Do you not think that the number of reads and the reads vs UMI histogram could help in figuring the driver of this variation out? If yes, do you have an idea how to interpret this information?
I appreciate your answer too much, many thanks