10x Genomics Chromium single-cell RNA-seq data analysis options? 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?
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