SoupX and normalization in Seurat

constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

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SoupX and normalization in Seurat #104

Closed tkapello closed 2 years ago

tkapello commented 2 years ago

I was wondering how a SoupX'ed count matrix should be treated for downstream analysis with the Seurat pipeline. Seurat uses raw integers for normalization, would it be alright to use the corrected counts from SoupX as the input for normalization?

constantAmateur commented 2 years ago

The Seurat normalisation is conceptually similar to generating TPMs and so will work fine with a SoupX corrected count matrix.