This track displays predicted Centromere Dip Regions (CDRs) identified by centrodip using ONT long-read sequencing. CDRs are regions of reduced 5mCpG methylation within centromeric satellite arrays, marking sites of putative kinetochore binding and active centromere function.
Raw ONT reads were basecalled and CpG methylation-called using Dorado (v0.5.3, model: 4.3.0+5mCG_5hmCG). Reads were aligned to the matched assembly using minimap2 (v2.28; --mod-thresholds m:0.8 --filter-threshold C:0.5). Methylation pileups were generated using modkit pileup (v0.4.2). CenSat annotations filtered for "active_hor" entries were passed to centrodip (v1.0.0) with parameters: --window-size 10000 --prominence 0.25 --height 0.1 --broadness 0.9 --min-size 1000 --min-score 500 --cluster-distance -1.
Each entry represents a predicted CDR call. Regions are scored based on the depth and consistency of methylation depletion relative to the surrounding active HOR array.
The raw data and processed files are available at [https://github.com/ph09/t2t_marmoset].
Data generated by Julian Menendez, Miga Lab, UCSC [Biomolecular Engineering and Bioinformatics].