CDR-Finder

This repository contains a snakemake to identify and quantify hypomethylated regions within centromeres, or Centromere Dip Regions (CDRs; Gershman et al., Science, 2022).

This is done by:

• Bin into 5 kbp windows
• Intersect with ALR annotations from RepeatMasker
• Only take bins that fall below the threshold (median frequency in the bins annotated as “ALR”)
• Merge consecutive bins
• Filter for bins greater than 50 kbp

Input

• target_bed: BED file of target region coordinates
• meth_tsv: Nanopolish methylation frequency TSV
• rm_out: RepeatMasker .out file

Output

Based on the median methylation frequency across the region, identifies and bins regions with methylation frequency below median spanning >50 kbp.

results/{sample}_CDR.bed