DESeq2 DE gene expression of scRNA-seq pseudobulk
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Christian • 0
@christian-24246
Last seen 11 months ago

Dear all,

I am performing differential gene expression analysis of single-nuclei RNA-seq data with DESeq2 and pseudobulk counts per cell type. 3 groups, 4 samples per group.

The nuclei vary to some extent concerning their mitochondrial RNA counts. So, DESeq2 naturally produces the most significant genes to be mitochondrial.

Is there a way to include this as a covariate in the design formula or somewhere else and provide an additional column "percent.mitochondrial.RNA" in the colData?

Thank you, best, Chris

DESeq2 SingleCell • 321 views
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@mikelove
Last seen 6 hours ago
United States

You could include the percent mitochondrial in the design, but also, if you aren't interested in these genes, you could filter them before running DESeq2.

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