Question: singlecell RNAseq normalisation
gravatar for nadia_boufaied
17 months ago by
nadia_boufaied0 wrote:

Hi I am analysing singleCell RNAseq data, in one batch of cells I have more spike-in than in the others (a different concentration of spike_in has been added to the RNA). I was wondering what is the best procedure to normalise the data to be able to integrete these cells in the analysis thank you Nadia

rna-seq spike_in singlecell • 519 views
ADD COMMENTlink modified 17 months ago by Mo Heydarian830 • written 17 months ago by nadia_boufaied0
gravatar for Mo Heydarian
17 months ago by
Mo Heydarian830
United States
Mo Heydarian830 wrote:


There are currently no tools on to deal with spike-in based normalization. We hope to change this soon.

In your case you may want to perform some additional normalization in addition to normalizing to your spike-in. Have a look at the normalization methods and packages discussed in this open-access publication:

Good luck with you analysis!

Cheers, Mo Heydarian

ADD COMMENTlink written 17 months ago by Mo Heydarian830
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