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"| | |style="background-color: #F2F2F2" align="center"|[[File:Report.png|frameless|link={{#sub:{{FULLPAGENAME}}|0|-11}}]][[{{#sub:{{FULLPAGENAME}}|0|-11}}|Main project page]]<br />{{#if:{{#lnpreventry:{{FULLPAGENAME}}}}|[[File:Resultset_previous.png|frameless|link={{#lnpreventry:{{FULLPAGENAME}}}}]][[{{#lnpreventry:{{FULLPAGENAME}}}}{{!}}Previous entry]] }}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]][[File:Resultset_next.png|frameless|link={{#lnnextentry:{{FULLPAGENAME}}}}]]}} | ||
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== | ==Simulating evolution and then pooled sequencing== | ||
* | |||
* '''We start with a population of N individuals with a 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 W-F simulation with selection. | |||
Or, we may have to use [http://arxiv.org/abs/1310.3234 forqs]. | |||
* '''Simulate pooled sequencing''' | |||
(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> | |||
Latest revision as of 23:29, 26 September 2017
 Analyzing pooled sequenced data with selection
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 Main project page Previous entry
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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 W-F simulation with selection.
(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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