Removing RBC contamination in Seurat
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9 months ago
roberts ▴ 40

Hello! I got data back from cellranger output. It is obvious in it that there is significant RBC contamination. There is some hemoglobin genes (HBA, HBB, HBD, etc) among the significant genes of clusters. Is it possible to filter out cells expressing these genes in Seurat? Thanks!

Seurat RNA-Seq R • 634 views
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Entering edit mode
9 months ago

Sure. Just remove the clusters that have those as markers, though be warned that certain vascular/endothelial cell populations may have them as markers as well. Typically, RBCs cluster well on their own, so removing them is pretty simple. See ?SubsetData or check out the Seurat cheatsheet.

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