Running Cell Ranger software on Eddie compute cluster

This educational guide is freely available to University of Edinburgh staff and students. It is intended as an aid to submit jobs to Eddie making use of the Cell Ranger™ module. “Cell Ranger” is a trademark of 10x Genomics.

With a rapid growth in the development of next-generation sequencing (NGS) technologies, there is an increasing focus on the characterization of single cells for genomics, transcriptomics, and epigenetics. Single-cell RNA sequencing (scRNA-seq) allow researchers to uncover complex and rare cell populations, discover regulatory relationships between genes, and trace the trajectories of individual cell lineages in development. The scRNA-seq NGS technology allows scientists to reveal novel biological discoveries compared to traditional profiling methods that assess bulk populations like RNA-sequencing (RNA-seq).

The scRNA-seq protocol involves the single-cell isolation, library preparation and the computational analysis of output sequencing data. One available technology is the 10x Genomics scRNA-seq, the ‘Chromium single Cell 3’ Solution’. The data generated from the 10X Chromium platform can be easily analysed by their Chromium Single Cell Software Suite which includes Cell Ranger™ and Loupe™ Cell Browser - see workflow below. Here one of the CMVM researchers has shared a ‘cellranger count’ pipeline (which is one out of the 4 Cell Ranger™ pipelines) which can be used to perform alignment, filtering, barcode counting and unique molecular identifier (UMI) counting of the reads using the Chromium cellular barcodes to generate feature-barcode matrices, determine clusters, and perform gene expression analysis.

The pipeline includes guidance on how to submit a script in Eddie for Cell Ranger™ and is available as a downloadable document.

The pipeline makes use of the following resources:

• Cell Ranger™ module. This is currently installed on Eddie
• Sequencing raw data is required as an input for Cell Ranger™
  
• Eddie linkage to DataStore is needed if the sequencing raw data is stored on DataStore

Source: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

Eleni Papachristoforou, Digital Research Services Ambassador (April-July 2020) and Precision Medicine PhD student at the Deanery of Molecular, Genetic and Population Health Sciences in the Centre of Inflammation Research (CIR) was responsible for the adaptation of this training material to the Digital Research Services website.

Free or Paid for:

The 'Cell Ranger™ Script for Eddie' guidance document is free to use and available from the link above.

• Free educational resource available to staff and students with a University log-in
• The pipeline is available in a downloadable format
• Cell Ranger module is currently installed in Eddie