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README_atacseq.md

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README_atacseq.md

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atacseqdata

This folder contains a unified script to process L1-stage ATAC-seq peaks from eLife and bin them into normalized genomic intervals for downstream analysis.

📜 Pipeline Summary (process_atac_data.sh)

  1. Download & Format Peaks

    • Downloads eLife peaks (ce10)
    • Extracts enriched peaks and reformats as 4-column BED

  2. LiftOver to ce11

    • Converts coordinates to ce11 using UCSC liftOver

  3. Slop + Quartile Split

    • Slops ±925 bp → 2kb peaks
    • Sorts by enrichment → splits into quartiles
    • Sorts by coordinate and bins each into 200 windows

  4. Genic vs Intergenic Annotation

    • Reformats GTF-derived gene annotations
    • Applies 5′ slop (200bp) to genes
    • Labels genic+promoter (1) vs intergenic (2)
    • Splits peaks based on ≥60% overlap

  5. Final Binning

    • Bins each genic/intergenic category into 200 segments

⚙️ Requirements

  • bedtools
  • liftOver from UCSC tools
  • awk, wget, sort
  • Genome size file: ce11.chrom.sizes
  • Gene annotation BED (from WS295)

📦 Outputs

  • ce11_L1atacseqpeaks_2kb_*.bed: Slopped ATAC peaks
  • *_200bins.bed: Binned windows for metaprofile plotting
  • ce11_L1atacseqpeaks_genic.bed, intergenic.bed: Split peak files

Author

Cansu Kose, 2025 – UNC Chapel Hill | Sancar Lab