Frequently Asked Questions

Analysis


I got slightly different numbers than were in the tutorial

Tip: 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 As a result it gets outdated very quickly before we can update it :( But it’s ok!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

Tip: 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.



UCSC - I fetched data from a remote website but now I’m logged out of Galaxy and my data is gone?

Tip: 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

Tip: 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

Tip: 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

Tip: Using IGV with Galaxy

You can send data from your Galaxy history to IGV for viewing as follows:

  1. Install IGV on your computer (IGV download page)
  2. Start IGV
  3. In recent verions of IGV, you will have to enable the port:
    • In IGV, go to View > Preferences > Advanced
    • Check the box Enable Port
  4. 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 on local



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