Do we need to concatenate the two haplotypes for mapping steps

[amara86]

Hi
Do we need to concat the two haplotypes of the reference genome to map the HiC reads, or do we need to map HiC reads to individual haplotypes? Below are my reference genoem headers:

H1Chr1
H1Chr2 and so on
Hap2 looks like:
H2Chr1
H2CHr2 and so on
Regards,
Amara

[millanek]

Hi amara,

If you have a diploid assembly, I suggest you map just to one of the two haplotypes. I would just use H1Chr1, H1Chr2 and so on.

All the best,
Milan

[amara86]

Thanks!