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Is that possible that the percent.mito level is zero? I have done vlnplot and it shows that its percent.mito level is zero. Does that mean my mitochondrial gene didn't detect?

enter image description here

It is violin plot. And the command is: enter image description here

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  • $\begingroup$ Sorry hua, but I find it difficult to understand. Could you clarify what is "percen.mito" ? It seems like it should be a function or a property of your data but I'm not sure. Also, could you explain what is "VlnPlot" ? It seems like a violin plot, but I'm not sure, perhaps the image didn't get attached (upload just a link and we will add it). $\endgroup$ – llrs Aug 13 '18 at 15:57
  • $\begingroup$ Your genome likely doesn't title mitochondrial genes MT-something, so you'll need to change how mito.genes is created. $\endgroup$ – Devon Ryan Aug 14 '18 at 7:22
  • $\begingroup$ Is "percent.mito level" the percent of reads mapping to genes annotated as mitochondrial? Are the mitochondrial genes annotated? Note you have edit button you can use to improve your question. $\endgroup$ – Kamil S Jaron Aug 14 '18 at 9:19
  • $\begingroup$ You should put "Seurat" in your question, and add a Seurat tag. $\endgroup$ – swbarnes2 Aug 14 '18 at 16:25
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I've just come across a similar issue. It seems the mouse and human mitochondrial genes use mixed capitalizations. See the following PR for details:

https://github.com/Hoohm/dropSeqPipe/pull/43

Bottom line is, if you ignore the case in the grep pattern it might work (assuming you use human/mouse):

mito.genes <- grep("^mt-", rownames(shox2crepos_mtmg@data), value=TRUE, ignore.case=TRUE)
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    $\begingroup$ Thank you so much, I have solve this problem after your instruction. $\endgroup$ – hua Aug 14 '18 at 17:59
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The simplest answer is that the bit of code you copied from the Seurat vignette is not working on the gene names you have. Look at the code. If none of your gene names begin with "MT-", none will be identified as mitochondrial.

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