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Hello,
As per my previous issue I'm still strying to make a pseudo trio-binning.
I have some long read data, used to make a reference with hifiasm with Hi-C data because it's working well with this species.
I am reusing this data to create a pseudo maternal (ZW) and a pseudo paternal (ZZ) by removing sequences supposed to come from the W. Then i use hifiasm on the data with those pseudo parents (in this case, the "individual" is exactly the same as the maternal ZW because i extracted nothing). After that i use YAHS to scaffold with Hi-C data.
To chek how well are my new haplotypes, i'm mapping them on the reference (made with the same data) and everytime my hap1 is exactly the same as the reference, but my hap2 as holes.
I assume it is because hifiasm put what it does'nt figure out only in hap1. I saw this present in other issues.
Would it be possible to put those incertitudes in both haplotype instead of only one?
Or is it something else entirely?
Thank you for your time, and for this great tool.
The text was updated successfully, but these errors were encountered:
Hello,
As per my previous issue I'm still strying to make a pseudo trio-binning.
I have some long read data, used to make a reference with hifiasm with Hi-C data because it's working well with this species.
I am reusing this data to create a pseudo maternal (ZW) and a pseudo paternal (ZZ) by removing sequences supposed to come from the W. Then i use hifiasm on the data with those pseudo parents (in this case, the "individual" is exactly the same as the maternal ZW because i extracted nothing). After that i use YAHS to scaffold with Hi-C data.
To chek how well are my new haplotypes, i'm mapping them on the reference (made with the same data) and everytime my hap1 is exactly the same as the reference, but my hap2 as holes.
I assume it is because hifiasm put what it does'nt figure out only in hap1. I saw this present in other issues.
Would it be possible to put those incertitudes in both haplotype instead of only one?
Or is it something else entirely?
Thank you for your time, and for this great tool.
The text was updated successfully, but these errors were encountered: