Closed rrydbirk closed 1 year ago
Brief update on what worked for me in ranked order for best solution:
type = "Genes"
factor = 1
alpha = 0.1
In the end, I went from 60k+ barcodes to ~10k barcodes in four problematic snRNA-seq samples with high ambient RNA load.
At the moment, it's unrealistic to have samples with 10k++ cells/barcodes. Instead, having this many barcodes after
rank_barcodes()
could be a sign of wrong breakpoint estimation. The following calculations take forever to finish with this many barcodes.Perhaps introducing a sanity check, e.g. stop if more than 10~20k barcodes, could be an idea? Also, this should be accompanied by a parameter
force
or similar to ignore the check and instead introduce a warning.