- Prepare CHM13-v1.0 and CHM13-v1.1 FASTAs and the rDNA flanking region sequences wrt to each reference version (see
rdna_to_chain.sh
for details). - Run
rdna_to_chain.sh
to build the chain file, including rDNA flanking regions, from CHM13-v1.0 to CHM13-v1.1 and CHM13-v1.1 to CHM13-v1.0.
Outputs:
- v1.0_to_v1.1_rdna_merged.chain
- v1.1_to_v1.0_rdna_merged.chain