Question: Can cellranger aggr work for nuclei that have more sequencing depth?
Answer: Yes it is possible to aggr for nuclei datasets that have more sequencing depths. For the Gene Expression library, this is measured in terms of the average number of reads that are confidently mapped to transcriptome per cell and for the ATAC & Multiome library, this is measured in terms of median unique fragments per cell. Hence it is possible to compare samples even if the sequencing depths are different.
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Can we aggregate nuclei and cellular data on Cell Ranger aggr?
Products: Single Cell Gene Expression, Single Cell ATAC, Single Cell Multiome ATAC + Gene Expression
Last updated: June 2023