Single Nucleus Muscle NFR and Nucleosome QTL Analysis

This repository contains the code and data analysis pipelines for the paper:

Wang X Robertson C.C. et al.,.* bioRxiv (2025).

Overview

This project investigates genetic variation affecting chromatin accessibility and nucleosome positioning in human skeletal muscle using snATAC-seq data. We identify:

• nfrQTLs (nucleosome-free region QTLs)
• nucQTLs (nucleosomal region QTLs)

We also analyze their relationship to regulatory annotations, fine-mapped GWAS variants, eQTLs, and transcription factor binding.

Repository Structure

muscle_nfr_nucQTL/
├── bin/                    # All R and Python based codes we used
├── env/                    # yml files for the conda environments
├── nextflow/               # LDSC analysis from Varshney et al. 2024 paper
├── run_snakemake/          # Bash commands that help you run the snakemake files
├── smk/                    # Snakemake files that manage each step of our analysis
└── README.md               # Project overview and setup instructions

Requirements

This repository was developed using:

• R (≥ 4.2.3)

• Python (≥ 3.8)

• Snakemake (≥ 7.30.1)

• Nextflow (≥ 24.10.6)

• Common bioinformatics tools:

  • [QTLtools] (https://qtltools.github.io/qtltools/pages/basic_install.html)
  • Samtools
  • bedtools
  • MACS2
  • [UCSC.utils] (https://genome.axolotl-omics.org/util.html)
  • [deepTools] (https://deeptools.readthedocs.io/en/develop/index.html)

Additional dependencies can be found in the respective bin/ and smk/ folders.

Usage

Running a Snakemake Pipeline

To execute a Snakemake workflow, open and use the run.sh script from the run_snakemake directory:

bash run.sh <pipeline_name>

Where <pipeline_name> corresponds to one of the workflows in the smk/ directory. For example:

bash run.sh peakcall

This will run the pipeline defined in smk/peak_calling.smk.

Make sure you have configured paths and resources in the corresponding .yaml config file. You can also test your scripts by running:

bash dryrun.sh <pipeline_name>

Main Pipelines

• peakcall – Call NFR and nucleosomal peaks from snATAC-seq BAM files
• sample_prep – Partition the files for anlaysis
• QTLprep – Prepare files for the QTL scan
• QTLscan – nfrQTL and nucQTL scanning
• coloc_qtls – Colocalization analysis between the nfrQTLs and the nucQTLs
• cit – Causal inference analysis between nfrQTLs and nucQTLs
• coloc_gwas* – Colocalization analysis between the QTLs and the GWAS summary statistics
• motif_meme – Motif enrichment analysis for different stages

Notes

Some of the raw data used in this study are currently under controlled access. We are making our best effort to make all processed data and summary statistics publicly available in the near future.

Certain directories and file paths in the code may include date information. Please adjust paths and config settings based on your own computing environment.

Citation

If you use this code or refer to the analyses in this repository, please cite:

Wang X and Robertson C.C et al., ...

Contact

For questions or feedback, please contact: Alice Wang – xiaoouw [at] umich.edu Cassie Robertson - ccrober [at] umich.edu Stephen Parker – scjp [at] umich.edu

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