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

From OpenWetWare
Jump to: navigation, search
(Autocreate 2013/10/16 Entry for User:Hussein_Alasadi/Notebook/stephens)
 
(fix raw html notebook nav)
 
(12 intermediate revisions by one other user not shown)
Line 2: Line 2:
 
|-
 
|-
 
|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>}}
+
|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]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;}}{{#if:{{#lnnextentry:{{FULLPAGENAME}}}}|[[{{#lnnextentry:{{FULLPAGENAME}}}}{{!}}Next entry]][[File:Resultset_next.png|frameless|link={{#lnnextentry:{{FULLPAGENAME}}}}]]}}
 
|-
 
|-
 
| colspan="2"|
 
| colspan="2"|
 
<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
 
<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
==Entry title==
+
==Simulating evolution and then pooled sequencing==
* Insert content here...
+
 
 +
* '''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 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 ~ .

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 where

(2) (frequency of the ith SNP) ~