On-the-fly Analysis Help

NOTE
This option has been disabled since the browser is not longer maintained.
For an improved version, visit PopFly, the Drosophila population genomics browser.

Overview

The popDrowser can perform customized on-the-fly reanalysis on the available data via Gbrowse customized pluggins. The results can be displayed directly in the browser in graph format or in a new window in text format.

Available Analysis

At the moment there are available on-the-fly variation reestimations using the VariScan¹ software for this statistics:

Segregating Sites - S
Difering Sites betwen Ingroup-Outgroup - S_inter
Number of mutations - Eta
Number of singletons - Eta_E
Nucleotide diversity - Pi
Waterson's nucleotide diversity per site - Theta
Tajima's D
Fu & Li's D*
Fu & Li's F*
Divergence per site - K
Fu & Li's D
Fu & Li's F
Fay & Wu's H
Number of polymorphic sites used for LD test - LD_sites
D value
Absolute D value - |D|
D' value
Absolute D' value - |D'|
R square
Number of haplotypes - h
Haplotype diversity - Hd
Fu's Fs

Usage

1.- Select the pluggin in the dropdown menu available in the top search section of the Dgvbrowser. Select "On-the-fly Variation Estimates Download" for text results or "On-the-fly Variation Estimates Visualization" for graphic representation.

2.- Click the "Configure..." button to display the options window. You can customize these parameters:

Statistic
Sliding Window size (Default and Maximum value: One window with the whole visualized region size)
Jump size (Default and Maximum value: Sliding Window size)

3.- Click "Go" button and wait for the results.

4.- For next text results you must repeat steps 1 to 3. Next graphic results needs no more steps if the track is not closed, changes in the parameters or moving to other regions will be automatically visualized.

5.- Only for the On-the Fly Visualisation: If no graphic appears in the detail panel, check the bottom of the track list and make sure the "plugin:Variation Estimates Visualization" is enabled (Usally happens if in a previous session the on-the-fly track was used and closed).

Vilella, A, J., Blanco-Garcia, A., Hutter, S. and Rozas, J. (2005). VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data. Bioinformatics 21: 2791-2793. [link]