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lh3 / psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
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PSMC wrong #28

Open zhoutinggan opened 3 years ago

zhoutinggan commented 3 years ago

Excuse me, as shown in the figure below, the peak difference of the same species is too large. What is the reason? image image

zhoutinggan commented 3 years ago

The results obtained are very different, but the heterozygosity of the two species is not very different, and they are closely related species. I don’t know which link is the problem. Please help me to solve it. Thank you

Marlappp commented 3 years ago

Hi, did you manage to solve this? I have a similar issue, i.e, my psmcfa file contains only 1 scaffold instead 90 and the resulting plot looks a bit like this....

mariarecuerda commented 3 years ago

Hi, I'm having the same problem. I ran psmc with bam files generated with two different reference genomes, and with the less related reference genome I get the nice psmc plot and with the same species reference genome I get the wrong one. Any ideas about what can be causing this issue?

Thank you.