Difference between revisions of "Popgen"

Revision as of 12:41, 9 February 2016 (view source) Mbomhoff (Talk | contribs) m ← Older edit		Latest revision as of 17:17, 4 May 2016 (view source) Mbomhoff (Talk | contribs) m
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−	CoGe can generate basic population genetics summary statistics given a GVCF input file and an annotation genome.	+	CoGe can generate basic population genetics summary statistics given a GVCF input file and an annotated genome. <div style='color:red'>Note: This tool is in Beta Testing.  If you use it and have feedback, please email us.<br><br></div>
	== Summary Statistics ==		== Summary Statistics ==
−	Summary statistics computed per feature overall (gene, CDS, etc) and by 0/4-fold degeneracy (for CDS only):	+	These summary statistics are computed per feature overall (gene, CDS, etc) and by 0/4-fold degeneracy (for CDS only):
	* Nucleotide diversity (pi) - average number of pairwise differences between variant sequences		* Nucleotide diversity (pi) - average number of pairwise differences between variant sequences
−	* Watterson's theta	+	* Watterson's estimator (theta)
	* Tajima's D		* Tajima's D
	== Steps ==		== Steps ==
	===1.  Load a GVCF file===		===1.  Load a GVCF file===
−	See the [[LoadExperiment]] tool to load a GCVF file against an existing genome in CoGe.	+	See the [[LoadExperiment]] tool for loading a GCVF file against an existing genome in CoGe.
	===2.  Analyze Diversity===		===2.  Analyze Diversity===
−	In the resulting experiment's menu select "Analyze Diversity".	+	Once the GVCF experiment is loaded, navigate to the experiment view and select "Analyze Diversity".
−	[[File:Screen_Shot_2016-02-09_at_11.14.11_AM.png|300px|Diversity analysis menu option]]	+	[[File:Screen_Shot_2016-02-09_at_11.14.11_AM.png|400px|Diversity analysis menu option]]
	===3.  Open the finished result===		===3.  Open the finished result===
	Open the result  in the PopGen tool to see results in tabular and graphical form.		Open the result  in the PopGen tool to see results in tabular and graphical form.
−	[[File:popgen_example_table.png|thumb|left|300px|Example table of summary statistics]]	+	[[File:popgen_example_table.png|thumb|left|400px|Example table of summary statistics]]
	[[File:popgen_example_plot.png|thumb|left|300px|Example plot of selected summary statistics]]		[[File:popgen_example_plot.png|thumb|left|300px|Example plot of selected summary statistics]]
		+
		+	<div style="clear:both"></div>
		+	==Troubleshooting==
		+	=== No results ===
		+	Check that the chromosome/contig names in your GVCF data file exactly match those for the genome.

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Latest revision as of 17:17, 4 May 2016

CoGe can generate basic population genetics summary statistics given a GVCF input file and an annotated genome.

Summary Statistics

These summary statistics are computed per feature overall (gene, CDS, etc) and by 0/4-fold degeneracy (for CDS only):

• Nucleotide diversity (pi) - average number of pairwise differences between variant sequences
• Watterson's estimator (theta)
• Tajima's D

Steps

1. Load a GVCF file

See the LoadExperiment tool for loading a GCVF file against an existing genome in CoGe.

2. Analyze Diversity

Once the GVCF experiment is loaded, navigate to the experiment view and select "Analyze Diversity".

3. Open the finished result

Open the result in the PopGen tool to see results in tabular and graphical form.

Troubleshooting

No results

Check that the chromosome/contig names in your GVCF data file exactly match those for the genome.