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Question: singlecell RNAseq normalisation
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gravatar for nadia_boufaied
17 months ago by
nadia_boufaied • 0
nadia_boufaied • 0 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
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modified 17 months ago by Mo Heydarian ♦ 830 • written 17 months ago by nadia_boufaied • 0
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gravatar for Mo Heydarian
17 months ago by
Mo Heydarian ♦ 830
United States
Mo Heydarian ♦ 830 wrote:

Hello,

There are currently no tools on useGalaxy.org 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: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0927-y

Good luck with you analysis!

Cheers, Mo Heydarian
ADD COMMENT • link written 17 months ago by Mo Heydarian ♦ 830
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