OSCAR

Ollie's Single Cell Analysis for the Romagnani Lab

OSCAR is a comprehensive pipeline designed for processing single-cell RNA, ATAC, and multiome sequencing data.

Features

• Comprehensive metadata tracking: Generate your metadata file here and keep track of sequencing runs.
• FASTQ demultiplexing and QC: Takes a raw bcl folder and demultiplexes FASTQ files, performs fastqc and multiqc.
• scRNA pipeline: Utilises cellranger for counting (with and without ADT/HTO), performs ambient-RNA correction with CellBender, and donor genotyping demultiplexing with cellsnp-lite and vireo.
• scATAC pipeiline: Utilises cellranger for counting, AMULET for doublet prediction, donor genotyping demultiplexing with cellsnp-lite and vireo, and for ASAP-seq performs ADT/HTO counting with kallisto.
• Multiome pipeline: All of the above
• Multiple sequencing run integration: Integrate sequenced libraries from several runs into one output folder.

Getting Started

To get started with OSCAR, please follow these instructions:

1. Clone the repository:

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

2. There are two Apptainer images: oscar-count.sif for the counting steps, and oscar-qc.sif for post-counting steps.

   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 are also required, and build steps can be found under reference/.

   For any questions, please e-mail me at oliver.knight@charite.de!