Can I still detect ambient RNA if I do not have filtered gene-barcode matrix?

Question

[SupBioInformatics]

Hi,

I am learning processing scRNA-seq data. I notice the ambient RNA is important metrics to QC and I found SoupX is the tool to detect ambient RNA. However, I realize I only have raw gene-barcode matrix, but lacks of filtered gene-barcode matrix, which is required for SoupX input.

Can I still detect ambient RNA if I do not have filtered and raw gene-barcode matrix?

Thank you in advance!

Answer 1

[Friederike]

The filtered gene-barcode matrix is usually processed by CellRanger where they try to guess which droplets contain sufficient amounts of RNA to indicate that they contained live cells (instead of just empty droplets with ambient RNA). You can generate your own filtered matrix by using the elbow plot approach by DropletUtils as described in the OSCA book.

[SupBioInformatics]

great! Thanks. I will check this out!