Question: Removing RBC contamination in Seurat
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gravatar for roberts
27 days ago by
roberts30
roberts30 wrote:

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!

rna-seq seurat R • 98 views
ADD COMMENTlink modified 27 days ago by jared.andrews077.9k • written 27 days ago by roberts30
1
gravatar for jared.andrews07
27 days ago by
jared.andrews077.9k
Memphis, TN
jared.andrews077.9k wrote:

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.

ADD COMMENTlink written 27 days ago by jared.andrews077.9k
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