Frequently Asked Questions
Tip: If a Tool is Missing
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 GTN-in-Galaxy 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.
How can I adapt this tutorial to my own data?
If you would like to run this analysis on your own data, make sure to check which V-region was sequenced. In this tutorial, we sequenced the V4 region, and used a corresponding reference for just this region. If you sequenced another V-region, please use an appropriate reference (either the full SILVA reference, or the SILVA reference specific for your region). Similarly, the
Screen.seqsstep after the alignment filtered on start and end coordinates of the alignments. These will have to be adjusted to your V-region.
Where can I read more about this analysis?
This tutorial was adapted from the mothur MiSeq SOP created by the Schloss lab. Here you can find more information about the mothur tools and file formats. Their FAQ page and Help Forum are also quite useful!