Owl

Cell Ranger

The cellranger pipeline runs Cell Ranger to process single-cell data.

Cell Ranger is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.

Currently we implement the cellranger count method that takes FASTQ files from and performs alignment, filtering, barcode counting, and UMI counting. It uses the Chromium cellular barcodes to generate feature-barcode matrices, determine clusters, and perform gene expression analysis.

Requirements

  • The Cell Ranger software and reference data must be available to the pipeline in a mounted volume. By default cellranger is located in /soft/cellranger/bin/cellranger. Use the soft argument in the pipeline definition file (see below) to change it.

Install 

curl -O https://raw.githubusercontent.com/eddienko/owl-cellranger-pipeline/main/owl_cellranger/cellranger.yaml
owl admin pdef add cellranger.yaml

Pipeline Definition File

An example pipeline definition file is:

# Version of the configuration file
version: 1

name: cellranger

# Location of the cellranger software
# soft: /soft/cellranger
# command to run, currently only count
command: count
# Arguments for the command above
id: SITTF9
sample: SITTF9
transcriptome: /storage/shared/cellranger_refs/refdata-gex-mm10-2020-A
fastqs: /storage/user/cellranger/SLX-20946
output_dir: /storage/user/cellranger/runs

# extra
# useful to add localcores and localmem in case cellranger fails to detect them
extra: ["--localcores", "20", "--localmem", "64"]

requirements:
  workers: 1
  cores: 25
  memory: 64

GitHub

← CITE-seq-Count