User: hern.moral

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hern.moral0
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Posts by hern.moral

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Comment: C: popoolation parallelization problem
... Just following up this threat, have you figured it out? I'm looking to do something similar. Can you explain how you implemented the parallelisation? Did you breakup the sync file in chunks and send individual jobs? ...
written 2.5 years ago by hern.moral0
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Answer: A: Lositan; spiky confidence interval, too many outliers
... Thanks for the detailed answer Tiago. I think the key point lands on the difference between populations and genetic clusters. It seems fair enough to use sampling populations in this case, but it would be handy to be able to test few (3 or less) genetic clusters to each other, because is at that lev ...
written 4.9 years ago by hern.moral0
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Answer: A: Lositan; spiky confidence interval, too many outliers
... Hello, thanks Tiago! Yes , 76 samples, they have similar number of samples across populations. These are screenshots of the GUI when data is uploaded.  When 2 populations (structure result) are defined in the genepop file: http://tinypic.com/r/nq1xk3/8 this is the one that gives the weird result: ...
written 4.9 years ago by hern.moral0
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Answer: A: Lositan; spiky confidence interval, too many outliers
... Some improvement when the original file is divided in 9 populations, see fig. However still some spikes in low He and Fst. This was using expected pop=20 and subsamplesize= 50, assumed Fst 0.06.  Fig: http://tinypic.com/r/2mrsnef/8 However, if I use default parameters --> expected pops = 9  and ...
written 4.9 years ago by hern.moral0
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Answer: A: Lositan; spiky confidence interval, too many outliers
... Hello, Mean Fst= 0.05 Expected total of pops, I have used different values and get same results= 2, 10, 40 and 100 Mutation model= Infinite sites Sample size = 69 individual, 734 loci Cheers, ...
written 4.9 years ago by hern.moral0
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Answer: A: Lositan; spiky confidence interval, too many outliers
... Hello Tiago, Thanks for your quick reply. Yes my file has two populations, the sample size reported is 2 populations. I'm basing this in a preliminar structure and DACP analyses. However, I have played with the expected total pops quite a bit (2, 10, 20, 50, 100), and getting the same behaviour. Sh ...
written 4.9 years ago by hern.moral0
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Lositan; spiky confidence interval, too many outliers
... Hello everyone, Im using Lositan with 734 SNP's for 72 individuals across a latitudinal cline, maybe structured in 2 main clusters and possibly in IBD.  If I use few iterations the envelope looks good (50K) (Fig1), but with more (>500K) looks terrible (Fig2), too ragged, and too many outliers. ...
lositan outliers fst selection written 4.9 years ago by hern.moral0 • updated 3.6 years ago by amineimanifar19790

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Popular Question 4.9 years ago, created a question with more than 1,000 views. For Lositan; spiky confidence interval, too many outliers

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