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. This is another link to a similar site on the same server if the above one is giving you problems: Slower Chromosome 1.

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,” (though admittedly not as continuous as the JBrowse experience). 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!)

To make this work, you need to have the GFF file you created in the morning session on your computer. Since I don't know if you do, hopefully everybody will be able to figure out how to do that. Save it to a place where you'll be able to find it.

Once you done that, go to http://gbrowse.gmod.org/fgb2/gbrowse/arabidopsis. Near the top of the page, there is a link for a tab called "Upload and Share Tracks." Click on that and there is a simple interface for uploading supported files. Clicking on "From a file" will give a normal "browse" button to find the file on your computer. When you select the file and click the upload button it will, it will show a spinner while it uploads, and then give you a status report (the size of the file uploaded, and links to edit the uploaded file and the created configuration). It will also automatically load the track into GBrowse, and clicking on the Browser link will take you back to the browser display. If you see the track, but no features in it, be sure to navigate to where in the genome that the features are. Try this link if you don't know where to look:

 http://gbrowse.gmod.org/fgb2/gbrowse/arabidopsis/?start=950000;stop=1050000;ref=NC_003070.9

Going back to the upload tab, you can click the "edit" link for the configuration and see some of the adjustable parameters to make it look different, by changing things like the fill color (bgcolor) or the picture used for the features (glyph). For a list of commonly used parameters, take a look at:

 http://gbrowse.gmod.org/gbrowse2/annotation_help.html#customize

If you run into problems and want to start over, you can use this link:

 http://gbrowse.gmod.org/fgb2/gbrowse/arabidopsis/?reset=1

which will throw away the uploaded file and restore the default settings.

A few comments about the GFF produced this morning

The GFF produced this morning looks like this:

NC_003070.9  cashx_gff    ABRF_Test    1455221 1455257 .    -    .    ABRF_Test;Note Mismatch=0
NC_003070.9  cashx_gff    ABRF_Test    1200379 1200415 .    -    .    ABRF_Test;Note Mismatch=0
NC_003070.9  cashx_gff    ABRF_Test    1170111 1170147 .    -    .    ABRF_Test;Note Mismatch=0
NC_003070.9  cashx_gff    ABRF_Test    1017175 1017211 .    -    .    ABRF_Test;Note Mismatch=0

Sharing tracks with other users (customers)

Any track (one that is "part of" the server or uploaded by a user) can be shared with other users, in two different ways. One is to get a URL that can be mailed to a user to click on it and be taken to the same view that the sharer sees, and the other is to "export" the track so that it can be viewed in a GBrowse instance on another server.

Sharing

To share a track, you can click on the concentric circle icon in the track name (it looks like an RSS feed icon). This will pop up a window that offers two URLs. The first one is the one we are currently interested in. If you copy that url, it can be sent in an email to someone else, can click on it and see the same track you are looking at. The url will look something like this:

 http://gbrowse.gmod.org/fgb2/gbrowse/arabidopsis/?eurl=http://gbrowse.gmod.org/fgb2/gbrowse/arabidopsis/?gbgff=1%1Dq=$segment%1Dt=abrf_test_cashx_gff_ada658_ABRF_Test.gff_1%1Ds=1%1Duuid=ada658bfdafea163504bcea3cf562942

This can also be done in a secure way (password protected), but the gbrowse.gmod.org server isn't set up for that. See the section below for a description of that.

Exporting

This is a little more sophisticated, and we can't see an example of it in this course, but had the GFF that was created in the morning session used "Chr1" instead of the NCBI id, we could have exported our track and viewed it in TAIR's GBrowse instance. What this does

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