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lh3 / psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
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Conspecific reference genome #15

Open davidaray opened 4 years ago

davidaray commented 4 years ago

I'm curious if this process works when one maps the reads to a reference genome for another species. For example, we have low-coverage reads (``14x) for one species and have inferred a reference-based assembly by mapping reads to a de novo assembly for a second species of the same genus.

Would you recommend using the reads mapped to the reference or the reads mapped to the inferred genome? Or, are both of these bad options?

Thanks.

David

lh3 commented 4 years ago

Try both and see if there are large differences first.