HapHiC

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pore-C data

23

Hello, @zengxiaofei Can HapHiC input porec data? If not, what adjustments do I need to make? Thank you in advance for your response

socialhang

How to correctly reassignment？

2

Hello, Xiaofei. I'm having some small issues with HapHiC. My species is an autotetraploid (2n=4x=44), and I used p_utg generated by hifiasm as the input file. When clustering, the command...

zjygoo

How to improve allotetraploid scaffolding in haphic?

13

Hi , I used haphic for allotetraploid genome (2n=4x=44). It makes 22 groups like the following which have huge variations in chromosome sizes as given below and can be seen...

RezwanCAAS

Work with hifiasm using haplotype-specific data

11

Hello @zengxiaofei , I used hifiasm with hifi and HiC data, and generate haplotype-specific data, including p_ctg.fa, p_utg.fa, r_utg.fa, and hap*.p_ctg.fa. As you mentioned in the tutorial, if I want...

chenzixi07

Perform not so good for haplotype mixed assembly

21

Hi, I am trying to use HapHiC to anchor a haplotype-collapsed genome (hifiasm p_ctg), and I found that HapHiC perform not so good, **especially contig ordering,** HiC data was mapping...

xiekunwhy

BED file support

3

Hi there Is it possible to implement support for BED files along with BAM and PAIR formats? Best regards

amvarani

How to set the chromosome number if I use p_ctg.fa from hifiasm when running haphic pipeline

2

Thank you for your excellent work! I wonder if I run the haphic pipeline correctly. I have a genome of 4G (a diploid, 2n=26), and I just use the p_ctg.fa...

utpala101

Question for Work with hifiasm

5

Hello, I have a question regarding the use of haphic for genome assembly and processing results with hifiasm. The genome I'm working with is diploid, and the haploid chromosome number...

lijl459

Haphic plot question

5

Hi, When I ran "/path/to/HapHiC/haphic plot out_JBAT.FINAL.agp HiC.filtered.bam", a very Hi-C contact maps appeared. Oddly, this is not the case in Juicebox. [contact_map.pdf](https://github.com/user-attachments/files/16632032/contact_map.pdf)

majssssa

Wrong assembly of X chromosome

1

I use haphic to anchor a genome to chromosome level but the results may be wrong. The X chromosome was not successfully assembled.

gotouerina