Centromeric Satellite Regions
The start and end of each region is defined by centromere haplotypes (as published relative to GRCh38 coordinates).Langley, Sasha A., et al. "Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA." Elife 8 (2019): e42989. Figure_2-source_data_1. The start and end (10 kb windows) cenHaps coordinates from hg38 were mapped to t2t-chm13.20200727 using minimap2. If alpha satellite was identified outside of the cenHap then the window was extended to end on the alpha monomer. In the case of acrocentrics (where no cenhap data is available), the acrocentric region is defined starting at base 1 and continuing to 2Mb past the last annotation of alpha satellite
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Data is available on globus: team-satellite/t2t-chm13.20200727.cenRegions.bed
Karen Miga