Answers.Body: <p>No in general cellranger does not remove doublets. You can apply a tool like <a href="https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.scrublet.html" rel="nofollow noreferrer">Scrublet</a> in scanpy or <a href="https://github.com/chris-mcginnis-ucsf/DoubletFinder" rel="nofollow noreferrer">Doubletfinder</a> in Seurat to infer doublets based on a mixed-transcriptional signal.</p>
  <p>I say in general because cellranger does detect certain types of doublets in two contexts:</p>
  <ol>
  <li>Multi-species experiments, e.g. the so-called <a href="https://kb.10xgenomics.com/hc/en-us/articles/360001074271-Does-Cell-Ranger-automatically-exclude-doublets-" rel="nofollow noreferrer">barnyard experiment</a>, cellranger detects cross-species doublets</li>
  <li>With <a href="https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/cellplex-metrics" rel="nofollow noreferrer">CellPlex</a> sample multiplexing, cellranger detects cross-tag (cross-CMO) doublets</li>
  </ol>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-08-23T19:59:41.507Z
Answers.LastActivityDate: 2022-08-23T20:04:42.907Z
Answers.LastEditDate: 2022-08-23T20:04:42.907Z
Answers.UserDisplayName: Chris_Rands
Body: <p>I noticed the tutorials that Scanpy and Seurat use do not demonstrate doublet removal in their down stream analysis.
  Is the dataset output of cellranger count already doublet removed or do I need to incorporate doublet removal before doing quality control etc?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-08-23T04:06:29.140Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-08-23T08:32:09.730Z
Comments.Text: CellRanger [doesn't remove doublets](https://kb.10xgenomics.com/hc/en-us/articles/360001074271-Does-Cell-Ranger-automatically-exclude-doublets-). Also, there is no doublet remotion in the tutorials of Scanpy, if you want to apply doublet filtering you should use `sc.external.pp.scrublet()`. I'm not sure about Seurat.
Comments.UserDisplayName: zorbax
Tags: <scrnaseq><transcriptome><10x-genomics>
Title: Are the doublets in the tutorial dataset in Scanpy/ Seurat already filtered?
ThreadText: # Are the doublets in the tutorial dataset in Scanpy/ Seurat already filtered?
  
  (Asked by: username_0 on 2022-08-23)
  
  I noticed the tutorials that Scanpy and Seurat use do not demonstrate doublet removal in their down stream analysis.
  Is the dataset output of cellranger count already doublet removed or do I need to incorporate doublet removal before doing quality control etc?
  
  **Tags:** scrnaseq, transcriptome, 10x-genomics
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: CellRanger [doesn't remove doublets](https://kb.10xgenomics.com/hc/en-us/articles/360001074271-Does-Cell-Ranger-automatically-exclude-doublets-). Also, there is no doublet remotion in the tutorials of Scanpy, if you want to apply doublet filtering you should use `sc.external.pp.scrublet()`. I'm not sure about Seurat.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2022-08-23. Score: 2
  
  No in general cellranger does not remove doublets. You can apply a tool like [Scrublet](https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.scrublet.html) in scanpy or [Doubletfinder](https://github.com/chris-mcginnis-ucsf/DoubletFinder) in Seurat to infer doublets based on a mixed-transcriptional signal.
  
  I say in general because cellranger does detect certain types of doublets in two contexts:
  
  1. Multi-species experiments, e.g. the so-called [barnyard experiment](https://kb.10xgenomics.com/hc/en-us/articles/360001074271-Does-Cell-Ranger-automatically-exclude-doublets-), cellranger detects cross-species doublets
  2. With [CellPlex](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/cellplex-metrics) sample multiplexing, cellranger detects cross-tag (cross-CMO) doublets
  
  
  ---
  
  