Genome Browsers

Table Of Contents

1. Introduction
2. IGV
3. UCSC

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1.  Introduction

This FAQ fragment covers the use of genome browsers with data produced by the NGSC.

The NGSC has long provided its own genome browser, TessLA, which offered access to data generated by the NGSC and cataloged by investigation, data type etc. However, TessLA is difficult to use with third-party data and its features have been superceded by other public browsers. TessLA will be discontinued on January 15, 2018.

The common alternative browsers are IGV and UCSC.

IGV is a browser that is downloaded to your desktop or laptop computer and runs using your computer's resources to display the data. You can either load local files that you download or load files that are located on the web. It provides access to many common data sources located on the web.

UCSC is a genome browser that runs in your web browser so it has a small 'footprint'. Data can either be uploaded to UCSC for display or pointed to via a URL. It contains a large amount of public data.

The NGSC's support for these browsers has been developing slowly. Both browsers can use data located at NGSC via URLs pasted one at a time into the browser. We are gradually developing more convenient ways of accessing the data.

Note that for both browsers you will have to provide your NGSC username and password to let the browser access the data. For IGV, the password is kept locally. For UCSC, the password is stored at UCSC so possibly represents a mild security risk.

2.  IGV

NGSC's support for IGV is as follows.

File-by-File Loading

• Resources are stored in a folder called IGV in your download area.
• There is one IGV folder per investigation, i.e., not on per PI.
• The IGV/Tracks or IGV/Links folder will contain links to you data.
• For convenience we may point to the same data in different ways, e.g., by sample number and by sample name or experimental condition name.
• You can load a track using the File / Load from URL ... option.
• Find the track URL in your web browser, copy it, then paste into IGV.
• IGV will prompt you for your NGSC username and password.

Scripts

We will typically generate a script to load a set of data at once.

• The IGV/Scripts scripts folder contains scripts to load many tracks at once.
• To use an IGV script, download it then run it in IGV using the Tools / Run Batch Script menu option.

An IGV script can not specify the color other attributes of a track so you must set these yourself.

Sessions

IGV can store the look and feel for a set of tracks in a session file. These are just plain text XML files. We expect to be able to generate these in the near future, but they are not available yet.

Server

IGV also offers the ability to read data via the File / Load from Server ... option. This option can be used with NGSC data, but it requires you to modify your IGV configuration and for NGSC to produce a description of the data we can serve to you.

We have used this in limited cases, but at the moment requires manual effort on our part to maintatin. We are working to automate the process.

3.  UCSC

We will not provide a full description of all of the options for UCSC here.

File-by-File Loading

Like in IGV you can ask UCSC to display data by providing a URL where the data can be found. Use your web browser to locate a file in the NGSC download area. (The IGV/Tracks folder may work for this.) Then cut and paste the file's URL into UCSC. You will have to add your NGSC username and password into the URL. See here for more information.

Track Hubs

UCSC has the concept of track hubs which are similar to IGV server files. We have generated these in the past but have not rolled the out as a standard feature.