Frequently Asked Questions
Where can I read more about Quality Control of data?
I really like QCFAIL, It has some nice user stories of quality control issues encountered in real data and experiments
Tip: MultiQC error for your FastQC reports?
Please double-check that:
- You selected
FastQCtool as the source of the log files in MultiQC.
- And you provided the Raw Data of FastQC and not the HTML reports.
Tip: When I get a warning for base per sequence content, what should I do?
So far it does not mean that your data is bad. Your protocol or your data might have a bias that you normally expect. Check first the following things:
- Adapter content (maybe some adapters are still in your data)
- Kmer content/Over represented sequences (this would indicate a contamination or a protocol/sequence bias)
- Per base quality plot. If the overall quality is not good, then probably the sequencing was poorly performed.
- Read about your protocol, e.g., ChIP-Seq and ATAC-Seq typically have a nucleotide bias. For example this article about ATAC-Seq.
Tip: If a Tool is Missing
To use the tools installed and available on the Galaxy server:
- At the top of the left tool panel, type in a tool name or datatype into the tool search box.
- Shorter keywords find more choices.
- 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:
- 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
- Use the Tutorial mode feature
- Open your Galaxy server
- Click on the curriculum 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)
- Still not finding the tool?
- Ask help in Gitter.
Tip: Troubleshooting errors
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.
- Expand the red history dataset by clicking on it.
- Sometimes you can already see an error message here
View the error message by clicking on the bug icon galaxy-bug
- Check the logs. Output (stdout) and error logs (stderr) of the tool are available:
- Expand the history item
- Click on the details icon
- Scroll down to the Job Information section to view the 2 logs:
- Tool Standard Output
- Tool Standard Error
- Submit a bug report! If you are still unsure what the problem is.
- Click on the bug icon galaxy-bug
- Write down any information you think might help solve the problem
- See this FAQ on how to write good bug reports
- Click galaxy-bug Report button
- Ask for help!