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(Simulating evolution and then pooled sequencing)
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|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Analyzing pooled sequenced data with selection</span>
 
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> Analyzing pooled sequenced data with selection</span>
|style="background-color: #F2F2F2" align="center"|<html><img src="/images/9/94/Report.png" border="0" /></html> [[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>[[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]]<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]]<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html>}}
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==Simulating evolution and then pooled sequencing==
 
==Simulating evolution and then pooled sequencing==
  
* '''We start with a population of N individuals with a certain SNP distribution <math> P(M)</math> ~ <math> N(\mu, \Sigma) </math>.'''
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* '''We start with a population of N individuals with a SNP distribution <math> P(M)</math> ~ <math> 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).
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We can use Dick Hudson's MsSel (MS with selection) to generate a SNP distribution.
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* '''We then evolve the populations for g generations with selection for SNP j'''
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In MsSel, we can specify an allele frequency trajectory for a site. We can generate a trajectory based on a simple W-F simulation with selection.
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Or, we may have to use [http://arxiv.org/abs/1310.3234 forqs].
  
* '''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. Also Forqs was written in way with selection experiments in mind, they have functions such as "Quantitative Trait" that allows the user to define the fitness function in a complex way.
 
  
 
* '''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>
 
 
  
  

Latest revision as of 22:29, 26 September 2017

Owwnotebook icon.png Analyzing pooled sequenced data with selection Report.pngMain project page
Resultset previous.pngPrevious entry      

Simulating evolution and then pooled sequencing

  • We start with a population of N individuals with a 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) } .

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 W-F simulation with selection.


Or, we may have to use forqs.


  • 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}) }