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

Question

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?

Answer 1

Data preparation

Cell Ranger uses the Illumina sequencing output (.bcl) files

1. Make fastq files: cellranger mkfastq ==> .fastq

2. Prepare count matrix: cellranger count ==> matrix.mtx, web_summary.html, cloupe.cloupe

3. Optional: combine multiple matrix.mtx files (libraries): cellranger aggr

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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