Tian 2024 Data Repository

This repository contains code and data structure for importing and processing the Tian 2024 single-cell RNA sequencing data. The experiments in Tian et al. involve two similar single-cell RNA sequencing (scRNA-seq) experiments conducted on Human PBMC (Peripheral Blood Mononuclear Cells) from 16 individuals.

Data from the two experiments are labeled as:

• SRR31856734
• SRR31856747

The pipeline includes downloading raw data, converting to FASTQ files, preprocessing with Cell Ranger, and organizing processed data for downstream analysis.

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Directory Structure

After running the pipeline, the directory structure under the tian-2024 directory is organized as follows:

tian-2024
├── raw
│   ├── SRR31856734
│   │   ├── SRR31856734_S1_L001_R1_001.fastq
│   │   └── SRR31856734_S1_L001_R2_001.fastq
│   ├── SRR31856747
│   │   ├── SRR31856747_S1_L001_R1_001.fastq
│   │   └── SRR31856747_S1_L001_R2_001.fastq
│   └── refdata-gex-GRCh38-2020-A
├── processed
│   ├── SRR31856734
│   │   ├── outs
│   │   │   ├── metrics_summary.csv
│   │   │   ├── filtered_feature_bc_matrix.h5
│   │   │   ├── molecule_info.h5
│   │   │   └── other_files...
│   ├── SRR31856747
│   │   ├── outs
│   │   │   ├── metrics_summary.csv
│   │   │   ├── filtered_feature_bc_matrix.h5
│   │   │   ├── molecule_info.h5
│   │   │   └── other_files...

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Pipeline Options

You can run the pipeline either in a single step or split into two steps:

Option 1: One-Step Execution

To run the entire pipeline (downloading and processing) in one step, use:

qsub -l m_mem_free=64G integrated_pipeline.sh

Option 2: Two-Step Execution

You can also run the pipeline in two separate steps:

Step 1: Download Data

qsub download_data.sh

Step 2: Process Data

After the data has been downloaded, process it with:

qsub -l m_mem_free=64G process_data.sh

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How to Run

1. Clone the repository:

   git clone [email protected]:Katsevich-Lab/import-tian-2024.git
   cd import-tian-2024

2. Set up the environment: Ensure .research_config contains the following:

   export LOCAL_TIAN_2024_DATA_DIR="/path/to/tian-2024/"

3. Submit the job: Use one of the pipeline options above to run the workflow.

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Notes

• Ensure all dependencies are installed and accessible in your $PATH:
  • prefetch, fastq-dump, cellranger, and wget.
• Sufficient memory (≥64GB recommended) and disk space are required to process the data.

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Citation

If using this pipeline or data for your work, please cite:

• Tian et al., 2024: DOI: 10.1038/s41588-024-02019-8

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