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Dear Steve,
The cellranger pipeline doesn't finish because the task qcScatterPlots stops after line 104 of the qc_scatterplots.R script, giving the error "invalid class "GFFFile" object: undefined class for slot "resource" ("characterORconnection")". I'm sorry, I'm not sure what the problem is and how to fix this, I hope you can fix this at some point, although it is not urgent.
Best wishes,
Erinke
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