Body: <p>I recently performed single cell RNA seq using core services and the web summary output from 10x that they have given shows that there are very few cells detected (100-300) cells per sample. Once this same issue happened in 1 out of 3 samples and this time it happened with 4 out of 4 samples.</p>
  <p>What might be the issue? The core says the cell preparation was not good but the cells were sorted for viability and then used to make the library. Any help?</p>
  <p>Full Summary snap:</p>
  <p><a href="https://i.sstatic.net/ywJQT.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/ywJQT.png" alt="enter image description here" /></a></p>
  <p>I have uploaded the full html file here : <a href="https://drive.google.com/file/d/11eQduL4OC4kjC0BfhGp3Nhoci69bRAy6/view?usp=sharing" rel="nofollow noreferrer">https://drive.google.com/file/d/11eQduL4OC4kjC0BfhGp3Nhoci69bRAy6/view?usp=sharing</a></p>
  <ul>
  <li>For one sample, Cell ranger 7.0.1 gave 284 cells while 6.8.2 gave 2200 cells.</li>
  </ul>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-06-18T19:32:12.397Z
Comments.Text: Very odd, can you say something about the say something about the sample type?
Comments.UserDisplayName: Chris_Rands
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-06-18T19:33:25.047Z
Comments.Text: Also cellranger 6.8 does not exist to my knowledge ;) can you check that
Comments.UserDisplayName: Chris_Rands
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-06-18T19:35:24.037Z
Comments.Text: I suggest runnnjng fastqc and maybe some Samtools modules then multiqc to aid diagnosis
Comments.UserDisplayName: Chris_Rands
Tags: <single-cell><cellranger>
Title: Cell Ranger returns too few cells!
ThreadText: # Cell Ranger returns too few cells!
  
  (Asked by: username_0 on 2023-06-16)
  
  I recently performed single cell RNA seq using core services and the web summary output from 10x that they have given shows that there are very few cells detected (100-300) cells per sample. Once this same issue happened in 1 out of 3 samples and this time it happened with 4 out of 4 samples.
  
  What might be the issue? The core says the cell preparation was not good but the cells were sorted for viability and then used to make the library. Any help?
  
  Full Summary snap:
  
  [![enter image description here](https://i.sstatic.net/ywJQT.png)](https://i.sstatic.net/ywJQT.png)
  
  I have uploaded the full html file here : <https://drive.google.com/file/d/11eQduL4OC4kjC0BfhGp3Nhoci69bRAy6/view?usp=sharing>
  
  * For one sample, Cell ranger 7.0.1 gave 284 cells while 6.8.2 gave 2200 cells.
  
  **Tags:** single-cell, cellranger
  
  > **Comments:**
  > **username_1**: Very odd, can you say something about the say something about the sample type?  
  > **username_1**: Also cellranger 6.8 does not exist to my knowledge ;) can you check that  
  > **username_1**: I suggest runnnjng fastqc and maybe some Samtools modules then multiqc to aid diagnosis  
  
  ---
  
  ## 0 answers
  
  