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Ollie's Single Cell Analysis for the Romagnani lab (OSCAR)

OSCAR - The best boy

OSCAR is a comprehensive pipeline for single-cell sequencing analysis, developed for the Romagnani lab at Charité. It provides tools and workflows for processing CITE-seq, DOGMA-seq, ASAP-seq, and Tapestri experiments.

Quick Start

1. Clone the Repository

cd $HOME/work/bin/
git clone https://github.com/ollieeknight/OSCAR

2. Download Apptainer Images

There are two Apptainer images:

  • oscar-count.sif - For counting steps
  • oscar-qc.sif - For post-counting quality control
mkdir -p ${TMPDIR}/OSCAR
apptainer pull library://romagnanilab/oscar/oscar-count:latest --dir ${TMPDIR}/OSCAR/
apptainer pull library://romagnanilab/oscar/oscar-qc:latest --dir ${TMPDIR}/OSCAR/

3. Reference Genomes

Reference genomes are also required. Build steps can be found under the reference/ directory.

Features

  • Automated Metadata Generation - Create standardized metadata files for your experiments
  • Feature Barcode References - Generate barcode references for Cell Ranger, Kallisto, and Tapestri
  • Streamlined Processing - Bash scripts to automate the entire workflow
  • Quality Control - Comprehensive QC steps built into the pipeline

Supported Assays

  • CITE-seq - Cellular Indexing of Transcriptomes and Epitopes by Sequencing
  • DOGMA-seq - DNA, Oligonucleotide, Gene expression, and Methylation Analysis
  • ASAP-seq - ATAC with Select Antigen Profiling by sequencing
  • Tapestri - Single-cell DNA and protein sequencing

Getting Help

For questions, suggestions, or issues:

Next Steps