<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>

CC BY-SA 4.0
2022-08-23T19:59:41.507Z
2022-08-23T20:04:42.907Z
2022-08-23T20:04:42.907Z
Chris_Rands
<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>

CC BY-SA 4.0
2022-08-23T04:06:29.140Z
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.
Community
CC BY-SA 4.0
2022-08-23T08:32:09.730Z
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.
zorbax
<scrnaseq><transcriptome><10x-genomics>
Are the doublets in the tutorial dataset in Scanpy/ Seurat already filtered?
# 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.  

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## 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


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