User:Hussein Alasadi/Notebook/stephens/2013/10/16: Difference between revisions

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* '''We then evolve the populations for g generations with recombination'''
* '''We then evolve the populations for g generations with recombination'''
To do this we can use Kessner's [http://arxiv.org/abs/1310.3234 Forqs]. Forqs allows the user to specify the recombination rate file. Which might be useful in the future.
To do this we can use Kessner's [http://arxiv.org/abs/1310.3234 Forqs]. Forqs allows the user to specify the recombination rate file which might be useful in the future.


* '''Simulate pooled sequencing'''
* '''Simulate pooled sequencing'''
(1) draw a coverage from <math> Pois(\lambda) </math> where <math> \lambda \approx 40-50 </math>




Revision as of 21:48, 16 October 2013

Analyzing pooled sequenced data with selection <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>

Simulating evolution and then pooled sequencing

  • We start with a population of N individuals with a certain SNP distribution [math]\displaystyle{ P(M) }[/math] ~ [math]\displaystyle{ N(\mu, \Sigma) }[/math].

To do this we can use Dick Hudson's MS to lay down neutral variants (but the distribution really does not matter).

  • We then evolve the populations for g generations with recombination

To do this we can use Kessner's Forqs. Forqs allows the user to specify the recombination rate file which might be useful in the future.

  • Simulate pooled sequencing

(1) draw a coverage from [math]\displaystyle{ Pois(\lambda) }[/math] where [math]\displaystyle{ \lambda \approx 40-50 }[/math]





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