The QC pipeline needs to be updated to handle single nuclei (sc)RNA-seq from 10xGenomics data.
Fastq generation should be the same as for scRNA-seq data so the changes will be in the QC pipeline, specifically the single library analyses will need a special "pre-mRNA" reference instead of the standard ones from 10xGenomics. The pre-mRNA references need to generated manually using cellranger mkref:
pjbriggs
commented
4 years ago
The QC pipeline needs to be updated to handle single nuclei (sc)RNA-seq from 10xGenomics data.
Fastq generation should be the same as for scRNA-seq data so the changes will be in the QC pipeline, specifically the single library analyses will need a special "pre-mRNA" reference instead of the standard ones from 10xGenomics. The pre-mRNA references need to generated manually using
cellranger mkref:https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references#premrna