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Interpreting a possible haploid #147
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Hi Jacqueline, smudgeplot find all the k-mer pairs that are similar to each other (i.e. different by 1 nt) and generates this plot out of it while guessing the 1n coverage. Basically what these two plots give you together, that there is no peak ~100x, all the k-mer pairs that are similar to each other have 200x coverage each - suggestion that that's the 1n peak. And given how big it is, it's quite possibly a haploid genome (obviously, there are some exceptions, very heterozygous genomes can occasionally look like this as well, but I don't think it's your case) What's the species? |
Hi @KamilSJaron, |
Oooh, a rust fungus! Cool! Yeah, i would be comfortable thinking that. I would try to fit the haploid model in genomescope (-p 1) so you have a meaningful genome size estimate. Then keep an eye on the size of the assembled genome. if they would be a lot different you can post here again and we can give it a think again. |
Hi @KamilSJaron! |
Great, I will close for now, feel free to reopen |
Hi,
I'm having trouble understanding my smudgeplot.
We have some reasons to believe that our species' genome should be a haploid, but based on what you replied on another thread regarding the 1n coverage peak, we are no longer sure about the ploidy. Could you please help figure it out?
It's a fungal species that was sequenced using PacBio HiFi.
Our plot looks like this:
And this is the genomescope profile for the same genome:
If you could please help understanding this ploidy, it would be greatly appreciated.
Thanks so much!
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