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whether is normal hic contacts of two haplotypes ? #258

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JiaoLaboratory opened this issue Mar 9, 2022 · 1 comment
Open

whether is normal hic contacts of two haplotypes ? #258

JiaoLaboratory opened this issue Mar 9, 2022 · 1 comment

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@JiaoLaboratory
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Dear hifiasm develpoer;
I have used hifiasm and hic data to generate two haplotype contigs, and then used 3DDNA generated chromosomal-level haplotypes for a diploit genome (2x =500M, het=0.6%) ;
The hic contacts looks like this:
image
I have no idea whether it is normal hic contact,?
why do two haplotypes (i.e. chr1 and chr8 ) perform so much strong hic interaction ?
I mean the hic contacts between the two haplotypes is abnormal, whether or not?
Thank U for your advice !
@lh3 @chhylp123

@JiaoLaboratory JiaoLaboratory changed the title whether is normal hic contacts of of two haplotypes ? whether is normal hic contacts of two haplotypes ? Mar 9, 2022
@chhylp123
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It is hard to say. Probably you could follow the blog here: https://github.com/baozg/phased-assembly-check. I think it is reasonable, especially for debugging Hi-C phased assemblies.

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