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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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How to divide the raw Hi-C reads to two haplotype-specific Hi-C reads? #302

Open naturalstay opened 2 years ago

naturalstay commented 2 years ago

Hi, Thanks for you nice hifiasm! I have assembled two haplotypes using HiFi and Hi-C reads. Now I will scaffolded the two haplotypes using Hi-C data. Do I need to divide the raw Hi-C reads to two haplotype-specific Hi-C reads for scaffolding the two haplotypes respectively. If there is a need, how do you think it should be divided. Thanks! Look forward to your reply.

chhylp123 commented 2 years ago

It would be better to scaffold both haplotypes at once, this may fix some phasing errors caused by hifiasm.

naturalstay commented 2 years ago

Scaffolding both haplotypes at once? Do you mean to merge the two haplotypes into a fasta file and scaffold it? Such as cat hap1.fa hap2.fa > merge.fasta.

chhylp123 commented 2 years ago

Yes, I think so.

naturalstay commented 2 years ago

Well. Thank you for your reply.

wuhuwuks commented 1 year ago

I have the same problem with you. Could you please tell me if you have solved it according to the author's method? In addition, I would like to ask whether your Hi-C data measured both haploids or only one haploid Hi-C

naturalstay commented 1 year ago

My HiC data is diploid data with low heterozygosity. I try to divide the reads into two haplotype data by the quality of the alignment quality.

wuhuwuks commented 1 year ago

My hi-c data is that of one haploid. Do you know that the hi-c data of one parent can separate two sets of haploid