text: user15919: 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?
  
  user104: No in general cellranger does not remove doublets. You can apply a tool like Scrublet in scanpy or 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:
  
  Multi-species experiments, e.g. the so-called barnyard experiment, cellranger detects cross-species doublets
  With CellPlex sample multiplexing, cellranger detects cross-tag (cross-CMO) doublets
  
  
original_text: 15919: <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>
   104: <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>
  