Normalization read counts scRNA seq with spike ins

Question

[tetapunto]

Hi,

I'm working with data obtained with sc-RNA seq where we used ERCC spike In to control for transcriptional amplification. I have some troubles with read counts normalization.

My question is: Is it possible to normalize read counts from a cell with the sum of spike ins read counts in that cell?

[shunyip]

Your question sounds similar to SAMstrt. Maybe you can take a look.