Can't find a gene in single cell
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4 months ago
Chris ▴ 260

Hi Biostars,

I have single-cell data with wild type and knock-out gene A. When I open the loupe file of both wild type and knock-out, I can find gene A in both samples. However, when I use Findallmarker() on the Seurat object from wild type, I don't find gene A, even after setting logfc.threshold = 0 and minpct = 0.1. This made me very confused. Gene A should show in the wild type sample. Would you please have a suggestion? Sorry but I don't know anyone else to ask.

single-cell • 562 views
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Your gene is probably not differentially expressed in any identity group of your dataset

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Got it. Thank you so much. I will try with FindConservedMarkers(). Would you please have a suggestion to find gene A? FeaturePlot of gene A is not clear. Seem expression level of this gene is quite low.

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What do you mean by "find gene A" ? If it is lowly expressed, it is likely that it would not be a marker of any of your cells identity groups. You cannot force an analysis to make a gene as differentially expressed.

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I mean to find which clusters that gene express and the cell type of those clusters.

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