# Description

Centromere dip regions detected with CDR-Finder v1.0.4.

# Methods

CDR-Finder is a tool that detects centromere dip regions based on average CpG methylation.

ONT reads with the MM and ML tags were aligned to the genome assembly via minimap2 v2.28 with the lr:hq preset.
* minimap2 -ax lr:hq -y -t 4 -I 8g <assembly> <reads>

CDR-Finder's workflow:
1. Extract the sequence of interest from the assembly.
2. Pileup CpG modification from the aligned BAM in the region of interest with modkit v0.3.2.
3. Intersect the sequence with its methylation data.
4. Bin the region of interest into 5 kbp windows and calculate the mean methylation percentage.
5. Run RepeatMasker v4.1.0 on the sequence of interest to identify regions containing alpha-satellite repeats (ALR/Alpha)
6. For each alpha-satellite containing region:
    * Merge consecutive bins.
    * Detect valleys in average methylation percentage based on relative prominence.
    * Check sides of each found CDR, filtering other CDRs, to calculate its relative height.
    * Extend edges to mean signal and some number of standard deviations to get missed peaks.
    * Merge adjacent detected CDRs.

# Changelog

* 2025-04-04 - Changed centromeric regions coordinates for mPonPyg2 (chr22_hap1_hsa21) and mPonAbe1 (chr6_hap2_hsa7, chrY_hap2_hsaY)
* 2025-04-11 - Manually added missing CDRs missed by CDR-Finder due to length threshold.

# Credits

Keisuke K. Oshima <keith.oshima@pennmedicine.upenn.edu>, Glennis A. Logsdon <glogsdon@pennmedicine.upenn.edu>