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

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(Simulating evolution and then pooled sequencing)
(Simulating evolution and then pooled sequencing)
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(1) draw a coverage (n) from <math> Pois(\lambda) </math> where <math> \lambda \approx 40-50 </math>
 
(1) draw a coverage (n) from <math> Pois(\lambda) </math> where <math> \lambda \approx 40-50 </math>
  
(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 07:52, 17 October 2013

Owwnotebook icon.png Analyzing pooled sequenced data with selection <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
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Simulating evolution and then pooled sequencing

  • We start with a population of N individuals with a certain SNP distribution 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 P(M)} ~ 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 N(\mu, \Sigma) } .

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 (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 40-50 }

(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}) }