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Intersect Scripts

This folder contains a collection of SLURM-compatible bedtools intersect scripts designed to compare Damage-seq and XR-seq datasets with various genomic features including ATAC-seq peaks, histone marks, gene quartiles, and genome-wide bins.

Each script performs parallelized intersection analysis and outputs bin-level counts or filtered overlaps.

📜 Script Overview

Script Description
atacseq_intersect.sh Intersects Damage-seq and XR-seq .bed files with ATAC-seq peaks (all peaks, genic/intergenic, expression quartiles)
epigenome_intersect.sh Intersects Damage/XR .bed files (and their simulations) with 5kb binned ChIP-seq histone marks (H3K4me3, H3K4me1, H3K27me3, H3K36me3)
genebodyexpressionquartiles_intersect_fordamageseq.sh Intersects Damage-seq samples with gene body quartiles in a strand-specific way
genebodyexpressionquartiles_intersect_forXRseq.sh Same as above, but for XR-seq samples
genomewide2kbwindows_intersect.sh Intersects XR-seq samples with 2kb genome-wide windows and computes RPKM
TSSandTES_binnedfiles_intersect.sh Intersects Damage-seq and XR-seq samples with 100-bin TSS and TES windows (strand-specific)
TSSquartiles_binnedfiles_intersect_damageseq.sh Intersects Damage-seq with TSS-based expression quartiles (150 bins)
TSSquartiles_binnedfiles_intersect_XRseq.sh Intersects XR-seq with TSS-based expression quartiles (150 bins)

🧰 Requirements

  • SLURM job scheduler
  • bedtools
  • Properly formatted .bed files from Damage-seq and XR-seq pipelines
  • Pre-processed annotation BEDs for:
    • ATAC-seq (peak bins, quartiles)
    • ChIP-seq 5kb bins
    • TSS/TES regions
    • Gene body quartiles
    • 2kb windows

📁 Output

Each script writes to a dedicated ../output/ subdirectory. Files typically include:

  • *_readCount.txt: total lines in the input .bed (used for normalization)
  • *_intersect.bed: output from bedtools intersect -c
  • SLURM logs: slurm-*.out

🧪 Notes

  • Scripts use -F 0.5 or -F 0.2 overlap fraction and may use -s/-S for strand specificity.
  • Simulated data intersections are supported in epigenome_intersect.sh.

Author

Cansu Kose, 2025 – UNC Chapel Hill | Sancar Lab