Closed yesitsjess closed 3 months ago
Hi,
what is samps_dir
, and ncol(sce)
?
Hi, what is
samps_dir
, andncol(sce)
?
samps_dir
is a vector containing the sample directory names (as output by cellranger count
run)
[1] "SITTA8" "SITTB8" "SITTC8" "SITTD7" "SITTD8" "SITTE7" "SITTE8" "SITTF7" "SITTF8" "SITTG7" "SITTG8" "SITTH8"
> ncol(sce)
[1] 75861
It's always a good idea to read the "Getting started" documentation: https://plger.github.io/scDblFinder/articles/scDblFinder.html#multiple-samples
So run it sample by sample and not on the whole dataset. Thanks, I'll try it.
I'm getting 33.4% of my UMIs predicted to be doublets (27.5% when clusters=F) and I read somewhere in the region of 10% is more usual. Any suggestions on what might've caused this? Or comments on if I'm doing something wrong, please?
I've also tried quickly clustering myself (rather than using fastcluster) and still get 23.2% doublets called.
My dataset is basically all the same cell type so I would expect a low number of clusters - will this effect things? Also I haven't done any additional QC here, just output from
cellranger count
is being used (empty droplets filtered out). I was planning to import the doublet predictions fromscDblFinder
as a QC step in my main pipeline because I'm usingcellbender remove-background
and wasn't sure if this would render my counts incompatible with doublet detection.scDblFinder v1.16.0