C. elegans DNA Repair and Damage Analysis Pipeline

This repository provides a complete and modular pipeline for analyzing DNA damage and repair in Caenorhabditis elegans, including Damage-seq, XR-seq, ATAC-seq, ChIP-seq, RNA-seq, and annotation processing. Each module is stored in a separate folder with its own README.md explaining scripts, dependencies, and outputs.

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📁 Repository Structure

Folder	Description	Documentation
wormbaseWS295/	Processes WormBase WS295 GFF2 annotations into BED format	README_annotationprocess.md
xrseqdata/	Complete XR-seq processing and normalization pipeline	README_XRseq.md
damageseqdata/	Full Damage-seq processing including adapter trimming, filtering, and QC	README_damage_seq_pipeline.md
atacseqdata/	ATAC-seq peak reprocessing and binning by genic/intergenic regions or expression	README_atacseq.md
atacseqrawdata/	ATAC-seq peak calling and calling dyad centers via nucleoATAC	README_atacseq_raw.md
epigenome/	ChIP-seq raw processing, peak calling, and binned region generation	README_epigenome.md
RNAseqdata/	RNA-seq processing, TPM filtering, expression quartile assignment	README_rnaseq.md
intersect/	bedtools intersect scripts for combining Damage/XR-seq data with genomic features	README_intersect.md
nucleosomeplots/	Intersection to ATAC-seq peaks and dyad positions, power spectrum, snr and final visualization scripts (Python)	README_nucleosomeplots.md
plots/	Final visualization scripts (R and Python) for strand bias, TSS metaprofiles, clustering	README_plots.md

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⚙️ Dependencies

• Core tools: bedtools, samtools, bowtie2, cutadapt, macs2, STAR, deeptools, sra-tools
• R packages: ggplot2, dplyr, ggpubr, pheatmap, tidyr, wesanderson, ggthemes, purrr
• Python packages: pandas, numpy, matplotlib, scipy, seaborn (optional)

Tested on a SLURM-based HPC environment using the WBcel235 (C. elegans ce11) genome.

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📤 Upload Instructions

cd Celegans_DNARepair_Pipeline/
git init
git add .
git commit -m "Initial commit: modular DNA repair and damage pipeline"
git remote add origin https://github.com/YOUR_USERNAME/YOUR_REPOSITORY_NAME.git
git branch -M main
git push -u origin main

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👩‍🔬 Author

Cansu Kose, 2025 – UNC Chapel Hill | Sancar Lab Cem Azgari, 2025 – Sabancı University | Adebali Lab

If you use or adapt this pipeline, please cite appropriately or contact us via GitHub.