Entering edit mode
9.0 years ago
lovestowell
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10
I'm working with a panel of 13K SNPs generated using a modified ddRAD library prep. The two "populations" are survivors vs dead of the same inbred individuals. I'm trying to use Lositan to test for outlier loci between these two groups but as you can see below, I'm getting a crazy plot for He vs Fst. I don't think it reflects biology. So I'm wondering if ...
... there is a problem with the SNPs themselves? The samples are from a salmonid, so I've trying to deal with the problems posed by paralogy.
... there is a problem with Lositan and how its calculating Fst or He? Or with the genepop input?
Any insight would be appreciated!
can't see the image! :-)
Hi, have you figured out what's causing this strange Fst/He plot? I am getting a similar pattern
Hi,
I never did get a satisfactory answer to this question. I ended up concluding that it was a problem with the particular genome of my species and how it was sequenced (a salmonid with an ancient whole genome duplication, leading to an overrepresentation of many sequences in a MiSeq run) as well as the choice of individuals included (pure and hybrid offspring of a controlled cross between two divergent lineages). So the Lositan approach of He vs Fst might not have been the most appropriate for me. I ended up using a genome scan approach of He and Fst only. Good luck,
Sierra