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tangerzhang / ALLHiC

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
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Problem about mitochondrial genome #49

Closed DustinChen1986 closed 4 years ago

DustinChen1986 commented 4 years ago

Report a problem about mitochondrial genome inserted in to chromosome by ALLHIC. So the mitochondrial genome should be excluded from the fasta file for HIC assemble.

tangerzhang commented 4 years ago

Thanks for reporting this issue. It happens when the genome contains inserted mitochondrial sequences during evolution. Hi-C signals will be detected between the previously inserted mitochondrial sequences and isolated mitochondrial genome. I totally agree with you that it will be better to remove plasmid sequences before Hi-C scaffolding.