Could adaptor contamination and primer dimers lead to low number of cells detected during a single cell RNA sequencing ?

Question

[charlesgwellem]

I am a newbie to genome alignment. My colleague did a single cell RNA sequencing experiment and the sequencing facility sent a preliminary QC report reporting that there were adaptor contamination and primer dimers. The sequecing experiment proceeded without prior removal of the contaminants. I have attached the QC results from running cellranger counts Could the presence of adaptor contamination and primer dimers be the reason why a low number of cells were detected?

[ATpoint]

Unlikely I guess, adapters/primers bind to the flow cell and reduce the usable amount of reads but that is pretty much it. It is somewhat beyond me though why you would sequence a probably very expensive experiment without checking libraries on a Bioanalyzer yourself and then repeat bead cleanup until the adapters are removed. Usually one extra round is sufficient. Anyway, it seems your library is the problem, not the sequencing. People often do a shallow sequencing of their single-cell libraries to infer number of cells (and by this approximate quality) before going deep, maybe this is something you should consider in the future.