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

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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>.'''
* '''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).
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 [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 23:29, 26 September 2017

Analyzing pooled sequenced data with selection Main project page
Previous entry      

Simulating evolution and then pooled sequencing

  • We start with a population of N individuals with a SNP distribution [math]\displaystyle{ P(M) }[/math] ~ [math]\displaystyle{ 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 W-F simulation with selection.


Or, we may have to use forqs.


  • Simulate pooled sequencing

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

(2) [math]\displaystyle{ f_i }[/math] (frequency of the ith SNP) ~ [math]\displaystyle{ B(n, f_i^{true}) }[/math]



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