How to choose threshold for scrublet?

Question

[bioinfo]

Hello,

I am using scrublet to remove doublets from my data. I am following the tutorial here:https://github.com/swolock/scrublet/blob/master/examples/scrublet_basics.ipynb

I don't think that the automatic threshold detection worked well for my data. The threshold doublet score is set at 0.26 and the histograms look like this:

I tried different threshold values so I set it to 0.17 and 0.15 to see if the histograms would be improved. I thinks that the 0.15 looks the best but I was wondering if that seems too low.

This is 0.17

And this is 0.15

Thank you

Answer 1

[bk11]

It is recommended to choose the threshold expected_doublet_rate based on how many cells your recovered (# of Cell Recovered) from your single cell experiment.

https://uofuhealth.utah.edu/huntsman/shared-resources/gcb/htg/single-cell/genomics-10x

[bioinfo]

That is how I set the expected double rate. I was wondering about the threshold doublet score.