mitochondrial RNA percentage in bulk RNAseq data
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@335cd804
Last seen 19 days ago
United States

Hi,

I am analysing bulk RNAseq data of 86 samples by DESeq2. I really liked one feature of Seurat in scRNAseq analysis "mitochondrial content percentage" . Is there a simple way to extract "mt percentage" information from deseq2 object. Like

plotCounts(dds, gene="MT-", intgroup="Group")

FYI: My deseq2 object have gene symbols, so all mitochondrial genes have MT- as suffix.

thanks

rnaseqGene RNASeqR DESeq2 RNAseq • 146 views
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@mikelove
Last seen 3 days ago
United States

We don't have this functionality, but you can just do:

cts <- counts(dds, normalized=TRUE)[idx,]

Then plot as you like, e.g. you can do colSums() of this, etc.

idx is just the lines matching whatever pattern you want, see grep or grepl which you can run on rownames(dds). The dds object can be subset with numeric or logical indices.

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