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Hi-C sequence alignment and quality control
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All Hi-C datasets were processed using the Juicer pipeline67 or distiller v.0.3.3 (https://github.com/open2c/distiller-nf); reads with a mapping quality score <1 were filtered out and discarded. Reads were aligned against the X. tropicalis v.9.1, our assembled and v.10.0 reference genomes and the PacBio contigs, respectively. Replicates were merged by Juicer’s mega.sh script. All contact matrices used for further analysis were KR-normalized with Juicer v.1.5. VC_SQRT-normalized matrices were used when the KR-normalized matrix was not available.
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