haplotype resolved assembly
m-jahani opened this issue · comments
Hi,
I am working with HIFI+HiC haplotype resolved assembly with HIFIasm (both have been also scaffolded with HiC data). Based on BUSCO and Merqury results, assemblies contain ~%3-4 duplication. I want to run purge_dups to get the bed file for suspicious regions for false seg dups.
What's the best way to run purge_dups for each haplotype?
- Merge hap1 and hap2 and run purge_dups?
- Run purge_dups separately for each haplotype (the HIFI reads are the same for both haps)?
Thanks
In other words, How can I find the coordinates of remaining false duplications in a haplotype resolved assembly?
Hi~
I face the same problem just like yours,have you got the problem solved? Can you tell me your solution?
thank you so much