Provide an overview of 10x data analysis packages.10x provides Cell Ranger which prepares a count matrix from the bcl sequencer output files and other files (see bottom of page https://support.10xgenomics.com/docs/license for the programs it uses).What can we do with the output files?
10x Genomics Chromium single-cell RNA-seq data analysis options?
rna seq;r;bioconductor;scrnaseq;10x genomics
Data preparationCell Ranger uses the Illumina sequencing output (.bcl) filesMake fastq files:cellranger mkfastq ==> .fastqPrepare count matrix: cellranger count ==> matrix.mtx, web_summary.html, cloupe.cloupeOptional: combine multiple matrix.mtx files (libraries): cellranger aggrData analysisLoupe Cell Browser visualization of cloupe.cloupe filesCount table matrix.mtx analysis options:PythonR Cell Ranger R Kit: cellrangerRkit::load_cellranger_matrix() ==> ExpressionSetR Scater: scater::read10XResults() ==> SCESet objectR Seurat: Seurat::Read10X() ==> Seurat object