sc/snRNASeq using cell ranger parameters

Question

[Claire]

Hi All

I am using cellranger to analyze sc/snRNASeq data. I did the same steps as I normally do with scRNASeq. Do we need to do something different in case the data is sc/snRNAseq? I am getting warnings (attached) in the analysis that I need to tackle. Thanks

Answer 1

[rpolicastro]

With snRNA-seq you generally want to count introns also, since you expect to be capturing an erniched fraction of nascent RNA compared to scRNA-seq. For Cell Ranger I believe you need to include the argument --include-introns for this.

[Claire]

Got you. Thank you so much :)