I have sorted single cells in 10 96well plates and performed SmartSeq2. A couple of the plates had to be resequenced as the desired depth of 1Mreads/cell was not reached for a few of them. I am wondering if in my analysis I should merge the counts of the replicates for each cell or if I should treat them as separate. Here's a tSNE plot of the normalized data:
My question is : Should I merge the counts from 1 and 1R (and also 3,3R and 5,5R) in my count matrix or would that not change anything and I should just leave them as is?
Conceptually merging technical replicates for bulkRNA if they would cluster like this would kind of make sense, but I don't know much about single-cell RNA and what would be a sound approach here. Any help would be greatly appreciated.