README_annotationprocess.md

wormbaseWS295

This folder contains scripts used to process WormBase WS295 GFF2 gene annotation files for C. elegans.

Scripts

• 1_gff2bed.py: Converts WormBase WS295 .gff2 annotation files to BED format with chromosome mapping and gene feature extraction.
• 2_process_bed.sh:
  • Filters for long genes (default: >2kb) separated by at least 500 bp
  • Generates slopped BED files
  • Creates strand-aware 100-bin TSS and TES regions

Requirements

• Python 3
• bedtools
• Shell environment with awk, bash

Inputs

• c_elegans.PRJNA13758.WS295.annotations.gff2
• Chromosome size file (ce11.chrom.sizes)

Output

• Final processed gene BEDs and binned TSS/TES BED files

Author

Cansu Kose, 2025 – UNC Chapel Hill | Sancar Lab