CenSat Track Generated with CenSat Annotation Workflow
Alpha-Satellites - Annotated with Fedor Ryabov’s HumAS-HMMER and simplified into the following bins:
- Active alpha (active_hor)
- diverged HORS (dhor)
- monomeric HORs (mon)
- mixed alpha (mixedAlpha) - alpha regions that can't be sorted into above categories
Human Satellites 2 and 3 - Annotated with Nick Altemose’s HSAT2/3 script
Other Centromeric Satellite annotations - Annotated with RepeatMasker
- HSAT1A - SAR in DFAM
- HSAT1B - HSAT1 in DFAM
- Gamma - includes all GSAT and TAR1 in DFAM
- Beta - BSR, LSAU, and BSAT in DFAM
- CenSat - other centromeric satellites CER, SATR, SST1, ACRO, HSAT4, HSAT5, TAF11
Centromere Transition (ct)
Centromeres are defined by merging all above satellite annotations within 2MB (bedtools merge) and then identifying the region containing the active array. Any stretch of sequence not annotated within this region is marked "ct"
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