SPLIT-seq workflow?

[ohmstead]

Really appreciate this package and the polished documentation.

I have a question about running this on snRNA-seq libraries prepared through the Split-seq combinatorial barcoding protocol (via a Parse Biosciences kit).

Biological replicates from different samples (in my experiment's case, nuclei from different brains) have their transcriptomes reverse-transcribed in situ during the first round of barcoding and then are pooled together for subsequent barcoding rounds. The documentation says that doubletFinder should be applied to individual samples independently, using the example of performing it on different 10X lanes separately. Does this also apply to the aggregated nuclei from split-seq? All samples are prepared in the same library, so there shouldn't be substantial batch effect.