Question

sc/snRNASeq using cell ranger parameters

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3.7 years ago

Claire • 0

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) enter image description here in the analysis that I need to tackle. Thanks

scsnRNASeq cellranger • 1.5k views

ADD COMMENT • link 3.7 years ago by Claire • 0

score 3 · Accepted Answer · 2022-03-04

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3.7 years ago

rpolicastro 13k

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.

ADD COMMENT • link 3.7 years ago by rpolicastro 13k

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Got you. Thank you so much :)

ADD REPLY • link 3.7 years ago by Claire • 0