Data preparation
Cell Ranger uses the Illumina sequencing output (.bcl
) files
Make fastq files:
cellranger mkfastq
==> .fastq
Prepare count matrix: cellranger count
==> matrix.mtx, web_summary.html, cloupe.cloupe
- Optional: combine multiple
matrix.mtx
files (libraries): cellranger aggr
Data analysis
Loupe Cell Browser visualization of cloupe.cloupe
files
Count table matrix.mtx
analysis options:
Python
R
Cell Ranger R Kit: cellrangerRkit::load_cellranger_matrix()
==> ExpressionSet
R
Scater: scater::read10XResults()
==> SCESet object
R
Seurat: Seurat::Read10X()
==> Seurat object