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Unreasonably high doublets rate #69
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Hi,
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Thank you for the quick reply!
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Hi, |
Hi, Computationally, scDblFinder only knows the number of cells I recovered from 10X. Therefore, the expected doublet rate ( |
Hi, Yes, you have a lower recovery rate than expected. I'm really not an expert there, but in my experience this has typically been attributable to low cell viability and/or expired/contaminated reagents (e.g. the buffer), but you'd have better luck trying to understand this with wet lab people. Yes, scDblFinder estimates the |
Thank you very much, plger! |
Dear developers,
Thank you very much for developing this useful tool. I tried it on my dataset. I used the
samples = sampleID
argument. However, I still have >10% doublets rate, which is unreasonable. Could you help please?Here is my code:
Here are the numbers of cells for each sampleID:
I double checked in the resulting SCE object and the scDblFinder.sample equals the sampleID.
According to 10X, each sample at this cell number should contain <5% doublets: https://kb.10xgenomics.com/hc/en-us/articles/360001378811-What-is-the-maximum-number-of-cells-that-can-be-profiled-
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