User:Tara K. Luckau/Notebook/Team ConGen/2012/01/21: Difference between revisions

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==CNTI Acos5==
==How to FSTAT for F<sub>ST</sub> values and significance==




===PCR===
* spent some time compiling the useful parts of F-statistics output from FSTAT ... here's what I figured out ...
* [[Image:20120110_PCRa.png|800 px]]
* FSTAT v 2.9.3.2




===Gel===
===Formatting Data===
====MS Excel====
* first row can be anything (title your Genepop run, for example)
* second row is marker names, separated by commas
* third row is lthe word "POP" (or "Pop" or "pop"), to separate populations
* fourth row is data
** start with sample name - can use any character, including white space
** comma
** genotypes separated by white space
: [[Image:20120122_GenePopExcel.png|300 px]]


{| {{table}} style="text-align: center"
|-
! Pour !! Load !! Run
|-
| 270 mL 1x TAE + 5.4 g agarose || 2 µL gel load dye + 4 µL PCR product || 160 V
|-
| 27 µL GelRed || 6 µL ladder || 45 minutes
|}


====MS Word====
* copy data from Excel, Paste Special into Word
** as Unformatted Text
* Save As ...
** Plain Text (.txt)
:: [[Image:Screen shot 2011-08-18 at 16.12.49.jpg|300 px]]
** File Conversion: Latin-US (DOS), CR/LF
:: [[Image:Screen shot 2011-08-18 at 16.20.04.jpg|300 px]]


[[Image:20120110_Gela.png|800 px]]


* mispriming everywhere - primer pair not usable for CNHY
===Genepop on the Web===
* lots of mispriming, but may be able to use conditions indicated by orange face ([[Image:orangefrownyface.png|20 px]]), if needed, under stringent conditions
* [http://genepop.curtin.edu.au/ http://genepop.curtin.edu.au/]
* favorable conditions indicated by [[Image:greenhappyface.png|25 px]]
 
 
====Option 1: Hardy Weinberg Exact Tests====
=====Suboption 3: Probability Test=====
* will output Hardy-Weinberg chi-square test, along with significance
:: grouped by marker
:: grouped by population
:: overall
:: [[Image:20120122 GenePop13.png|500 px]]
 
 
====Option 5: Allele Frequencies, etc.====
=====Suboption 1:  Genotypic matrices, number obs/exp homozygotes and heterozygotes, allele frequencies, etc=====
* will output genotype matrix (how often one allele occurs with another), genotype frequences, expected and observed number of homozygotes and heterozygotes, allele frequences
* calculate H<sub>e</sub> and H<sub>o</sub>
:: <math>H_e = \tfrac{\mbox{expected number of heterzygotes}}{\mbox{number of samples}}\mbox{ . . . }H_o = \tfrac{\mbox{obvserved number of heterzygotes}}{\mbox{number of samples}}</math>
:: [[Image:20120122 GenePop51.png|500 px]]




Revision as of 19:29, 30 January 2012

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How to FSTAT for FST values and significance

  • spent some time compiling the useful parts of F-statistics output from FSTAT ... here's what I figured out ...
  • FSTAT v 2.9.3.2


Formatting Data

MS Excel

  • first row can be anything (title your Genepop run, for example)
  • second row is marker names, separated by commas
  • third row is lthe word "POP" (or "Pop" or "pop"), to separate populations
  • fourth row is data
    • start with sample name - can use any character, including white space
    • comma
    • genotypes separated by white space


MS Word

  • copy data from Excel, Paste Special into Word
    • as Unformatted Text
  • Save As ...
    • Plain Text (.txt)
    • File Conversion: Latin-US (DOS), CR/LF


Genepop on the Web


Option 1: Hardy Weinberg Exact Tests

Suboption 3: Probability Test
  • will output Hardy-Weinberg chi-square test, along with significance
grouped by marker
grouped by population
overall


Option 5: Allele Frequencies, etc.

Suboption 1: Genotypic matrices, number obs/exp homozygotes and heterozygotes, allele frequencies, etc
  • will output genotype matrix (how often one allele occurs with another), genotype frequences, expected and observed number of homozygotes and heterozygotes, allele frequences
  • calculate He and Ho
[math]\displaystyle{ H_e = \tfrac{\mbox{expected number of heterzygotes}}{\mbox{number of samples}}\mbox{ . . . }H_o = \tfrac{\mbox{obvserved number of heterzygotes}}{\mbox{number of samples}} }[/math]




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