chromosome number more tnan my species

[mengzhiyue-comeon]

After displaying the out_JBAT.hic file in Juicebox, it was found that it contains 13 chromosomes, which is more than the chromosome number of my species, which is 12. How can I solve this issue? The initial contig.fa file was generated by assembling two haplotypes using hifiasm. Can this software be used for haplotype phasing and scaffolding?

hic_data.docx

[c-zhou]

Hello @mengzhiyue-comeon,

This tool cannot be used to detect haplotype redundancies. You could try to align chromosmes to each other to check the synteny to see if there are duplcations.

I do not know what species it is. Is it possible it is a B chromosome? Or it is a sex chromocome?

Best, Chenxi

[mengzhiyue-comeon]

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