Answers.Body: <p>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:</p>
  
  <p><a href="https://github.com/Hoohm/dropSeqPipe/pull/43" rel="nofollow noreferrer">https://github.com/Hoohm/dropSeqPipe/pull/43</a></p>
  
  <p>Bottom line is, if you ignore the case in the grep pattern it might work (assuming you use human/mouse):</p>
  
  <pre><code>mito.genes &lt;- grep("^mt-", rownames(shox2crepos_mtmg@data), value=TRUE, ignore.case=TRUE)
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-08-14T17:59:49.253Z
Answers.Text: Thank you so much, I have solve this problem after your instruction.
Answers.UserDisplayName: hua
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-08-14T15:44:21.400Z
Answers.LastActivityDate: 2018-08-14T15:44:21.400Z
Answers.UserDisplayName: Sebastian Müller
Answers.Body: <p>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.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-08-14T16:28:07.340Z
Answers.LastActivityDate: 2018-08-14T16:28:07.340Z
Answers.UserDisplayName: swbarnes2
Body: <p>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?</p>
  
  <p><a href="https://i.sstatic.net/WvRfE.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/WvRfE.png" alt="enter image description here"></a></p>
  
  <p>It is violin plot. And the command is:
  <a href="https://i.sstatic.net/x4MoL.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/x4MoL.png" alt="enter image description here"></a></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-13T15:57:00.907Z
Comments.Text: 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).
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-14T07:22:26.277Z
Comments.Text: Your genome likely doesn't title mitochondrial genes `MT-something`, so you'll need to change how `mito.genes` is created.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-14T09:19:29.250Z
Comments.Text: 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.
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-08-14T16:25:30.220Z
Comments.Text: You should put "Seurat" in your question, and add a Seurat tag.
Comments.UserDisplayName: swbarnes2
Tags: <scrnaseq>
Title: SC-RNA seq percent.mito
ThreadText: # SC-RNA seq percent.mito
  
  (Asked by: username_0 on 2018-08-13)
  
  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](https://i.sstatic.net/WvRfE.png)](https://i.sstatic.net/WvRfE.png)
  
  It is violin plot. And the command is:
  [![enter image description here](https://i.sstatic.net/x4MoL.png)](https://i.sstatic.net/x4MoL.png)
  
  **Tags:** scrnaseq
  
  > **Comments:**
  > **username_1**: 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).  
  > **username_2**: Your genome likely doesn't title mitochondrial genes `MT-something`, so you'll need to change how `mito.genes` is created.  
  > **username_3**: 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.  
  > **username_4**: You should put "Seurat" in your question, and add a Seurat tag.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_5 on 2018-08-14. Score: 1 | Accepted answer
  
  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)
  
  ```
  
  > **Comments:**
  > **username_0**: Thank you so much, I have solve this problem after your instruction.  
  
  ---
  
  ### Answer by username_4 on 2018-08-14. Score: 1
  
  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.
  
  
  ---
  
  