Frequently Asked Questions

De novo transcriptome reconstruction with rna-seq

I’m using the same training data, tools, and parameters as the tutorial, but I get a different number of transcripts with a significant change in gene expression between the G1E and megakaryocyte cellular states. Why?

This is okay! Many aspects of the tutorial can potentially affect the exact results you obtain. For example, the reference genome version used and versions of tools. It’s less important to get the exact results shown in the tutorial, and more important to understand the concepts so you can apply them to your own data.


Support

I get a different number of transcripts with a significant change in gene expression between the G1E and megakaryocyte cellular states. Why?

Question: I get a different number of transcripts with a significant change in gene expression between the G1E and megakaryocyte cellular states. Why?

This is okay! Many aspects of the tutorial can potentially affect the exact results you obtain. For example, the reference genome version used and versions of tools. It’s less important to get the exact results shown in the tutorial, and more important to understand the concepts so you can apply them to your own data.


General Questions

Can't find one of the tools for this tutorial?

To use the tools installed and available on the Galaxy server:

  1. At the top of the left tool panel, type in a tool name or datatype into the tool search box.
  2. Shorter keywords find more choices.
  3. Tools can also be directly browsed by category in the tool panel.

If you can’t find a tool you need for a tutorial on Galaxy, please:

  1. Check that you are using a compatible Galaxy server
    • Navigate to the overview box at the top of the tutorial
    • Find the “Supporting Materials” section
    • Check “Available on these Galaxies”
    • If your server is not listed here, the tutorial is not supported on your Galaxy server
    • You can create an account on one of the supporting Galaxies screenshot of overview box with available Galaxies section
  2. Use the Tutorial mode feature
    • Open your Galaxy server
    • Click on the icon on the top menu, this will open the GTN inside Galaxy.
    • Navigate to your tutorial
    • Tool names in tutorials will be blue buttons that open the correct tool for you
    • Note: this does not work for all tutorials (yet) gif showing how GTN-in-Galaxy works
  3. Still not finding the tool?

Running into an error?

When something goes wrong in Galaxy, there are a number of things you can do to find out what it was. Error messages can help you figure out whether it was a problem with one of the settings of the tool, or with the input data, or maybe there is a bug in the tool itself and the problem should be reported. Below are the steps you can follow to troubleshoot your Galaxy errors.

  1. Expand the red history dataset by clicking on it.
    • Sometimes you can already see an error message here

  2. View the error message by clicking on the bug icon

  3. Check the logs. Output (stdout) and error logs (stderr) of the tool are available:
    • Expand the history item
    • Click on the icon
    • Scroll down to the Job Information section to view the 2 logs:
      • Tool Standard Output
      • Tool Standard Error
    • For more information about specific tool errors, please see the Troubleshooting section
  4. Submit a bug report! If you are still unsure what the problem is.
    • Click on the bug icon
    • Write down any information you think might help solve the problem
      • See this FAQ on how to write good bug reports
    • Click Report button
  5. Ask for help!


Still have questions?
Gitter Chat Support
Galaxy Help Forum