ABRF2010 Workshop

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GMOD Browser Tools and Exercises Workshop
Part of the Next Generation DNA Sequencing Analysis Satellite Meeting
ABRF 2010
3-4:30pm, 20 March 2010
Sacramento, CA, USA

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Workshop

Abstract

JBrowse is a free, open source, web-based browser for displaying and navigating genome features. It is part of the Generic Model Organism Database (GMOD) project which aims to provide reusable components for working with genomic data, and is in use by hundreds of organizations around the world. JBrowse is relatively easy to install and can display many types of genome feature. In this workshop, we will look at JBrowse both from the user perspective (how to upload data of various types) and from an administrator perspective (how to configure tracks and make them permanent). The workshop will also introduce GBrowse, GMOD's other genome browser, and SAMtools, an open source tool for working with large sequence alignments. The combination of SAMtools and JBrowse make an excellent platform for providing extra value to sequencing core lab customers.

GBrowse

About

GBrowse is the most widely implemented genome browser in use today, with several hundred known servers around the world. For this tutorial, we created a server at http://gbrowse.gmod.org/gbrowse2, and specifically, a GBrowse instance of A. thaliana Chromosome 1. You might want to open that in another tab now to follow along and try things out during this section.

Navigation and Searching

The primary way people “get into” GBrowse is by searching for a gene or other keyword. To search, the user just enters the text (gene name or other identifier, or something in the description) into the “Landmark or Region” box at the top of the display. Since we have arabidopsis data, we could try things like “AT1G01930” or “Chr1:100000..200000”. We can also do wild card searches, like “AT1G019*”, which will give a list of matches back that we can choose from.

Once looking at the GBrowse display, there are typically two or three graphical sections: the overview, region and details panel. The region panel is optional (and can be configured to be on or off by the administrator) and shows a “neighborhood” overview that doesn't cover as much area as the overview (which is always the full length of the chromosome or contig being looked at). While GBrowse has left and right pan buttons on the side of the details panel, and similar buttons along with a zoom menu above the overview panel, most people navigate GBrowse by click and drag selection on one of the scale bars for the chromosome at the top of each of panels. By pressing down on the left mouse button and moving the mouse over the region to be navigated to, GBrowse will either automatically go to the region selected, or depending on how GBrowse is configured, will pop up a menu to let the user choose what action to take. For example, in a sample yeast data set that comes with GBrowse, this is the menu that is give when the user selects a region in the details panel:

Details popup.png

When GBrowse navigates to a new location, it uses AJAX (Asynchonous Javascript and XML) to reload all of the tracks, so a complete page reload is not necessary, making the browsing experience more “continuous.” This same technology enables a few other niceties of GBrowse:

  • When new tracks are selected from the ones available in the list below the details panel, the new track is added without having to reload the page
  • Since the tracks are drawn separately, the can also come from different servers, giving GBrowse the ability to work with multiple rendering and database servers to make it faster than it would otherwise be with just one server.
  • The tracks can also be moved up or down relative to other tracks just by clicking on the name of the track and dragging it up or down.

Uploading user data

Several file formats are supported for upload to a GBrowse instance:

In the morning section of the tutorial, we created GFF (not GFF3), so we'll use that as an example of how to upload data. (This marks the first time the server we are using is being used by a classroom—so let's hope there are no fireworks!)

Sharing tracks with other users (customers)

Securing GBrowse and its data

Advanced topics

Installing and configuring GBrowse

Conference Talk

Seeing the Forest and the Trees: Visualizing Next Generation Sequence Data, by Mitch Skinner

Part of the Session Tools to Facilitate Management, Analysis and Visualization of 2nd Generation Sequencing Data
3:45pm - 5:00pm, Monday, March 22