Frequently Asked Questions
Analysis
I got slightly different numbers than were in the tutorial
This tutorial uses UCSC which is constantly updating it’s data! As a result it gets outdated very quickly before we can update it :( But it’s ok! It’s expected here to get different numbers.
History
My jobs are not running / I cannot see the history overview menu
Please make sure you are logged in. At the top menu bar, you should see a section labeled “User”. If you see “Login/Register” here you are not logged in.
Recommended browser
UCSC - I fetched data from a remote website but now I’m logged out of Galaxy and my data is gone?
This is a known bug with Chrome + Galaxy, we’re working on it galaxyproject/galaxy#11374. For now we can recommend using Firefox (known to work) or trying another browser.
User interface
I can’t find the “Analyze Data” button
The Galaxy interface has changed a bit recently, “Analyze Data” was always the home button, and now looks like a home icon.
My Galaxy looks different than in the tutorial/video
Galaxy gets frequent updates, different servers will be running different versions. This is nothing to worry about, just let us know if you can’t find how to perform a task in your Galaxy.
Visualisation
Using IGV with Galaxy
You can send data from your Galaxy history to IGV for viewing as follows:
- Install IGV on your computer (IGV download page)
- Start IGV
- In recent versions of IGV, you will have to enable the port:
- In IGV, go to
View > Preferences > Advanced- Check the box
Enable Port- In Galaxy, expand the dataset you would like to view in IGV
- Make sure you have set a reference genome/database correctly (dbkey) (instructions)
- Under
display in IGV, click onlocal