Question: Depth of Single Cell RNA seq experiment
gravatar for sch1
2.7 years ago by
sch110 wrote:


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.


rna-seq • 1.3k views
ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 2.7 years ago by sch110

If you have not seen this paper. With single cells other considerations will apply.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by genomax64k
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