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constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
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Can I still use SoupX to detect ambient RNA if I do not have filtered gene-barcode matrix? #67

Closed rrchai closed 3 years ago

rrchai commented 3 years ago

Hi,

I just realize the data I have only contains raw gene-barcode matrix, but lacks of filtered gene-barcode matrix. Can I still use SoupX to detect ambient RNA ?

Thank you!

constantAmateur commented 3 years ago

As this is a semi-regular request and I may include a function to do this easily in future versions. For now, look at the section "Profiling the Soup" in the vignette.

By aware that this approach explicitly assumes that the background profile is the same as the average expression across all cells. This is in general a reasonable assumption (see paper), but there will be inaccuracies as a result. In particular stress response genes like MT will likely have a higher background fraction than suggested by the average across all cells.