Frequently Asked Questions

Day 5: Choose your own adventure

Training session: 16S Microbial Analysis

Presentor: Saskia Hiltemann

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Q: My jobs are not running / I cannot see the history overview menu

A: 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.

Q: I can't find the make contigs tool

A: Make sure you add in a dot between "make" and "contigs" when you search in the tools: make.contigs

Q. After I run make.contigs, the group file seems to have lost the read name information

A: If you are using the Australian Galaxy server (usegalaxy.org.au), there is a different version of the make.contigs tool installed. So: when you run make.contigs, for "Renames sequences", set this to No. (The default is Yes).

Q. I can't run workflow 2 - Data Cleaning and Chimera Removal

A. If you are using the Australian Galaxy server (usegalaxy.org.au), this workflow may have a problem with the remove.seqs tool. Solution: Import the workflow (link in the tutorial). Edit. Click on the Remove.seqs tool box, which brings up the tool panel at the right. For Output logfile, select No. Save workflow.

Q. In the Taxonomy-to-Krona tool, I can't see the taxonomy file to load.

A.  Make sure to click on the sideways folder icon to specify that you are loading a "dataset collection". This is the third icon along under "Taxonomy file". The, the file should be visible and able to be selected.