Difference between revisions of "User:Hussein Alasadi/Notebook/stephens/2013/10/16"
(→Simulating evolution and then pooled sequencing) 
(→Simulating evolution and then pooled sequencing) 

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* '''We start with a population of N individuals with a certain SNP distribution <math> P(M)</math> ~ <math> N(\mu, \Sigma) </math>.'''  * '''We start with a population of N individuals with a certain SNP distribution <math> P(M)</math> ~ <math> N(\mu, \Sigma) </math>.'''  
−  +  We can use Dick Hudson's MsSel (MS with selection) to generate a SNP distribution.  
+  
+  
+  * '''We then evolve the populations for g generations with selection for SNP j'''  
+  In MsSel, we can specify an allele frequency trajectory for a site. We can generate a trajectory based on a simple WF simulation with selection.  
+  
+  
+  Or, we may have to use [http://arxiv.org/abs/1310.3234 forqs].  
−  
−  
* '''Simulate pooled sequencing'''  * '''Simulate pooled sequencing'''  
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(2) <math> f_i </math> (frequency of the ith SNP) ~ <math> B(n, f_i^{true}) </math>  (2) <math> f_i </math> (frequency of the ith SNP) ~ <math> B(n, f_i^{true}) </math>  
−  
−  
Revision as of 09:33, 17 October 2013
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Simulating evolution and then pooled sequencing
We can use Dick Hudson's MsSel (MS with selection) to generate a SNP distribution.
In MsSel, we can specify an allele frequency trajectory for a site. We can generate a trajectory based on a simple WF simulation with selection.
(1) draw a coverage (n) from Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle Pois(\lambda) } where Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle \lambda \approx 4050 } (2) Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle f_i } (frequency of the ith SNP) ~ Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle B(n, f_i^{true}) }
