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chris-mcginnis-ucsf / DoubletFinder

R package for detecting doublets in single-cell RNA sequencing data
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Which value is the cell loading density value? #100

Closed denvercal1234GitHub closed 3 years ago

denvercal1234GitHub commented 3 years ago

Hi everyone,

I hope to use DoubletFinder in my Seurat pipeline for scRNA-seq data from 3 donors of the same sorted cell population and cell type without any stimulation.

From various discussions, I understand the cell loading density is the density of cells loaded into the 10X microfluidics chip, used to sequence the data. This cell loading density value will correspond to an estimated doublet formation rate that is specific to my dataset. This rate is what we need to predict potential doublets.

However, when I looked at the outputs from the 10X Genomics Cell Ranger summary (estimated total cells = 13,400 cells), I cannot seem to find this value. Any pointer?

Thank you very much for your help!

chris-mcginnis-ucsf commented 3 years ago

Hi again @denvercal1234GitHub ,

Looks like you loaded the 10x lanes to yield ~4500 cells/lane. According to the 10x protocol, this means you should expect about a 3.5% doublet rate.

Chris