broadinstitute / CellBender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

https://cellbender.rtfd.io

BSD 3-Clause "New" or "Revised" License

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Do not output "cells" with zero counts #111

Open sjfleming opened 3 years ago

sjfleming commented 3 years ago

Occasionally we see a few droplets where the cell probability is high, but the posterior output counts are zero. Do not allow this to happen.

63

kseuro commented 3 years ago

Came here to post about this — I recently encountered this issue after running CellBender. ~900 / 100,000 called cells in my dataset have zero counts, the majority of which have less than 1000 UMIs. My stop-gap measure is to set a UMI cutoff at 1000 and simply continue the analysis, although I'll be keen to re-run CellBender once this bug is fixed.

giorgiatosoni commented 1 year ago

Same here! I just noticed that my cellbender output filtered files contain several "cells" with zero counts

maartenciers commented 9 months ago

I see the same around 2% of my nucleus data has this issue this only seems to happen with low quality cells less then 1000 UMIs. So It's not a bad thing to actually remove those cells as they are poor quality anyway.