-
Notifications
You must be signed in to change notification settings - Fork 18
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Doublet filtering in Parse Biosciences data #90
Comments
Hi, Is Parse the combinatorial indexing method (i.e. what used to be called split-seq before it was commercial)? If they did some assays with different amounts of loading you can perhaps use that to estimate an expected rate, but if not it's not a big deal, in a typical context the importance of the expected doublet rate. You can leave You can also have a look at the histogram of the doublet score, unless you have a very complex dataset one typically observes a very strong bimodal distribution, so that it doesn't matter much where exactly one sets the threshold in between. Hope this helps, |
Hi, Yes. It is four-step barcoding to label cells in different wells. I left I'll draw a histogram to see distribution of doublet rate, thank you for the suggestion. Best. |
Right, you probably do have a lot more cells than in a single 10x capture, right? |
The number of cells is 12k in data for now but data with ~ 1 million cells will be produced soon, so yes, number of cell will be way higher in Parse data compare to 10x. Once Here, density of doublet score across cells: It seems that doublet score is fairly discriminative between singlets and doublets by regarding histogram plot of doublet score. However, when I put score threshold of 0.598 manually, this ended up with almost the same number of doublets (2908) as what I found automatically with Best. |
I don't understand your question: the You've got very clear singlets and very clear doublets, and some ambiguous cells in the middle, which will be influenced by the thresholding. Where exactly you should place the threshold also depends on how bad missing doublets or singlets would be given your aims, but if you don't have strong opinion it's reasonable to leave it where the thresholding procedure set it. |
My expectation was higher threshold in detection of doublets, e.g., around 0.9 but I'm surprised that it was ~0.6. I agree on difference in threshold due to rounding. I see, I do not have strong opinion so I'll use Thank you! |
Hi,
I have single-cell Parse Biosciences data. I want to detect doublets in the data but I'm unsure what cutoff should be set up in
scDblFinder()
function. In Parse paper, authors claimed that doublet rates less than 3% even for 100,000 cells.I'm wondering what
dbr
anddbr.sd
arguments inscDblFinder()
function should be set up for Parse data or something else that you would suggest for this.Best regards.
~Kaan
The text was updated successfully, but these errors were encountered: