Entering edit mode
2.0 years ago
benjamin.pyenson
•
0
Hi,
I have run souporcell successfully on single-nucleus RNAseq filtered barcode (bc) matrix generated from CellRanger (v.6.1.2), which generates an experiment-wide ambient RNA % of 6.69 for k=10 predefined clusters. While I have created a custom-script to distinguish singlets from the unassigned and doublets in clusters.tsv, there does not seem to be a way to remove ambient RNA from each cell with the output and tools provided by souporcell. Has anyone found a way to do this?
As a result, I am looking to employ decontX, soupX, and/or CellBender as downstream analyses to then remove ambient RNA from the singlet barcodes.
Or, have others found that simply reporting a low ambient RNA % is sufficient?
Thank you,
