chhylp123
chhylp123
I see, thanks a lot. The UL-integration should be able to deal with this case reliably.
>1. Yes. >2. Either is fine. With or without Hi-C share same bin files.
I guess it should be better to do QC first. You can directly use PB official tools.
With '-l0', hifiasm would not enable purge_dups so that alternate contigs/haplotigs are kept in `p_ctg`. This is why `p_ctg` with `-l0` is significantly larger than `p_ctg` without `-l0`.
If hifiasm is run with `-l0`, then we have an assumption that this sample is homozygous. So in theory we shouldn't have any alternate contigs. `if those alternate contigs are...
I guess real samples cannot be fully homozygous? If you run hifiasm with `-l0`, `a_ctg` should be very small. Those contigs of `a_ctg` come from small bubbles. You can use...
~28 Mbp is very long so that it is hard for hifiasm to totally lose it even there is a bug. Can you find 3 copies in the `p_utg.gfa`? If...
@glogsdon1 Could you please also share the parental yak indexes?
@glogsdon1 Sorry for the delay. I will reach out to you this evening.