Hello,
I am new to this field, and would greatly appreciate an answer to this question.
I am looking at two highly similar populations of stem cells which I will have isolated by FACS. I want to perform single cell RNA seq on these cells in order to better understand the differences between these populations.
I understand that there is a trade off between the number of cells analysed and reads per cells. As my populations are so closely matched, I anticipate that I will have to deeply sequence my cells. What I am trying to understand is how can I calculate how many reads I will need per cell, and how many cells I will need to sequence in order to fully characterise my cell populations?
Many thanks for your help.
Sam
If you have not seen this paper. With single cells other considerations will apply.