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How to determine the "number of droplets captured" for doublet_number when using DoubletFinder? #54

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MorticiaGiulia opened this issue Aug 7, 2024 · 0 comments

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@MorticiaGiulia
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MorticiaGiulia commented Aug 7, 2024

Dear all, I'm rather new to scRNA-seq analysis and am even newer on the program DoubletFinder. I'm following the tutorial to run it on R. I got stuck when I read the Data section (under required), which stated:
" Expected number of doublets ($DOUBLETS)
This can be calculated based on the number of droplets captured using our [Doublet Estimation Calculator]

I went onto the [Doublet Estimation Calculator], and it asks me to put in the number of droplets captured.

I'm using the CellRanger output to create Seurat Objects. And my questions are:

  1. How can I get the number of droplets captured?
  2. Is it the number of cells (rows in the metadata) of the Seurat object created from the CellRanger filtered_feature_bc_matrix output?
  3. Or is it the number of cells from the CellRanger raw_feature_bc_matrix output?

Thank you very much for your time and support!

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