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sc/snRNASeq using cell ranger parameters

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
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written by Claire • Claire

1 answer

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.

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written by rpolicastro rpolicastro

Got you. Thank you so much :)

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written by Claire • Claire

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