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lh3 / psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
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psmc plot for reference individual looks different? #23

Open eggomez opened 3 years ago

eggomez commented 3 years ago

Hi there! We've done whole genome sequencing for six individuals of a species and one of the six was used to generate a reference assembly. We then ran the psmc on each of the six individuals (all mapped to this new reference). The plots for the five non-reference individuals look highly similar, but the individual (F6110) used for the reference is quite different (see plot below). Wondering if there is any technical reason why aligning to itself would affect things. In the meantime, I'm tryinging alingning them to a different genome to see how that affects things. Thank you for any thoughts!! mu3 g3 plot

CaprimulgusG commented 1 year ago

Hi @eggomez I don't suppose you ever managed to find a fix for this or the cause of the issue? I am having a similar issue at the moment also.