broadinstitute/CellBender

Background Fraction

hk2rma opened this issue · 2 comments

hk2rma commented

How to interpret the background fraction column included in the metadata,
Does a value of 0.5 mean that 50% of the contents of that cell are ambient RNA?
I couldn't find any documentation on this and a HTML file was not generated.

Thanks

bdferris642 commented

Also curious about this!

seyoon-lee commented

Adding on, I was wondering whether it would be plausible to remove cells with a high background fraction after running CellBender, or should I consider them ambient-free since CellBender would have already deducted the ambient reads?

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