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.