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constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
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On setting mouse transcripts as 0 in scRNA-Seq experiment #78

Closed Jay-Leung closed 3 years ago

Jay-Leung commented 3 years ago

Thank you for this useful package! I am new to scRNA-Seq and recently have acquired some data pertaining to Patient-Derived Xenografts. I was thinking to set the mouse genes to 0 to calculate ambient RNA expression - in the paper, the mouse genes were set to 0 in the human cells and vice versa, but I could not find the exact documentation for that. How would I know which genes are mouse specific? Thanks!

constantAmateur commented 3 years ago

If I have understood correctly, it sounds like you only interested in the human cells and not the native mouse cells. I would do the following:

  1. Run useToEst = estimateNonExpressingCells(sc, nonExpressedGeneList = list(mouseGenes = namesOfMouseGenesHere))
  2. Run sc = calculateContaminationFraction(sc, list(mouseGenes = namesOfMouseGenesHere), useToEst = useToEst)
  3. Calculate the corrected matrix as usual with adjustCounts
  4. Manually remove all the rows of the final matrix corresponding to mouse genes.