Hi Zechen!
I am trying to use the heterozygosity as and additional source of information from a RADseq dataset and I want to know if I can get the phased haplotypes while implementing Rainbow. As far as I understand, the heterozygous sequences are collapsed during the "Bottom–up merging process" (rainbow merge), but I wanted to know if there is a way to obtain the different haplotypes for each locus at any point?
According to the paper, the dividing procedure (top–down dividing clusters - rainbow div) could generate either true clusters or split clusters with separated heterozygous sites, and this module "was introduced to distinguish sequencing errors from heterozygote or variants between repetitive sequences". Thus, is it correct to assume that each cluster in this stage (after rainbow div) represents an haplotype? If so can they be obtained direclty from the output or is there any additional consideration to be done?
Thank you very much!
Catalina R-P
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You're correct. After the div step, you should get a very strict haplotype. But I don't know if the length of the haplotype meets your need. In addition, the divided clusters may not come from the same locus since the clustering may involve similar sequences of different loci.
Thanks,
Zechen
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi Zechen!
I am trying to use the heterozygosity as and additional source of information from a RADseq dataset and I want to know if I can get the phased haplotypes while implementing Rainbow. As far as I understand, the heterozygous sequences are collapsed during the "Bottom–up merging process" (rainbow merge), but I wanted to know if there is a way to obtain the different haplotypes for each locus at any point?
According to the paper, the dividing procedure (top–down dividing clusters - rainbow div) could generate either true clusters or split clusters with separated heterozygous sites, and this module "was introduced to distinguish sequencing errors from heterozygote or variants between repetitive sequences". Thus, is it correct to assume that each cluster in this stage (after rainbow div) represents an haplotype? If so can they be obtained direclty from the output or is there any additional consideration to be done?
Thank you very much!
Catalina R-P
Hi Catalina,
You're correct. After the div step, you should get a very strict haplotype. But I don't know if the length of the haplotype meets your need. In addition, the divided clusters may not come from the same locus since the clustering may involve similar sequences of different loci.
Thanks,
Zechen