search

schatzlab / genomescope

Fast genome analysis from unassembled short reads
Apache License 2.0
249 stars 56 forks source link

Triploid genome #140

Closed gunjanpandey closed 22 hours ago

gunjanpandey commented 1 week ago

This is not an issue but requesting help. Could you please help understand the genome situation in regard to the genomescope plot?

This is supposed to be a triploid lizard of around 2.5G. With hifi and HiC data, hifiasm is generating three haplotypes as below.

image image image image image

I appreciate your help.

mschatz commented 1 week ago

From the shape of the kmer profile (in blue, without any modeling) I would have guessed this to be a fairly heterozygous diploid as there are not three well defined peaks. If you truly have a triploid sample, from the overall shape, that would imply you have ~9x of each haplotype and these three haplotypes are quite different from each other, although there are some sequences that are shared between all three and some that are shared between two but not all three. Have you tried SmudgePlot - that would help visualize and interpret if there are 3 separate haplotypes. And when you align your haplotypes to each other, do you see significant differences between them? I would try rerunning as a diploid sample just to make sure hifiasm is correctly separating.

Good luck! Mike

On Wed, Sep 11, 2024 at 6:10 PM gunjanpandey @.***> wrote:

This is not an issue but requesting help. Could you please help understand the genome situation in regard to the genomescope plot?

This is supposed to be a triploid lizard of around 2.5G. With hifi and HiC data, hifiasm is generating three haplotypes as below. image.png (view on web) https://github.com/user-attachments/assets/f6809c25-377c-4c8e-b124-ad84805727c7 image.png (view on web) https://github.com/user-attachments/assets/0610c995-1ca7-4868-a1ba-581b2f0b0850 image.png (view on web) https://github.com/user-attachments/assets/4a5a49be-6037-43f4-be2c-224d5586c7b0 image.png (view on web) https://github.com/user-attachments/assets/9364667d-e2ec-48e3-ab28-37c2b96b5f2b image.png (view on web) https://github.com/user-attachments/assets/05fd61e3-27f5-4cc4-9597-735d69cbb0b7

I appreciate your help.

— Reply to this email directly, view it on GitHub https://github.com/schatzlab/genomescope/issues/140, or unsubscribe https://github.com/notifications/unsubscribe-auth/AABP345JBPUOPQNCD2TLTULZWC5XFAVCNFSM6AAAAABOB4IQDSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGUZDAOBXGY4DMMQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

gunjanpandey commented 22 hours ago

Thanks Mike,

This is a diploid lizard turning triploid so it would have a diploid pair + one extra set of chromosomes, we believe. I am yet to do the alignment.

Closing this thread with thank you.