On-the-fly Analysis Help

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:

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:

 

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).

 


  1. 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]