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
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