xQTL workbench - Tutorial for biologists: Running a basic QTL analysis
In the main menu, click on Run QTL mapping. In the this screen, leave Select compute resource on Local and click on Start new analysis.
Please note that many aspects of running an analysis are already outlined in xQTLBiologistRun, so here we will stick with a specific case for the tutorial data.
Step 1: Choose analysis
- Fill in a nice output name, e.g. 'yeast_qtl'.
- Leave Select the analysis on 'Rqtl_analysis'.
- Leave the amount of divided parts on 5, though you can select 2 if the machine you are working on is not very powerful, or 10 if you have a quad- or octocore machine. This is the amount of parallel processes that your analysis will be chopped up into, to reduce the time it needs to complete. (especially on a computer cluster)
- Click Next.
Step 2: Choose parameters
- In the dropdown for Select input data, genotypes, select '!ClusterDemo_yeast_geno'.
- In the dropdown for Select input data, phenotypes, select '!ClusterDemo_yeast_pheno'.
- Leave all settings under Select parameters on their defaults.
- Click Start.
The analysis is now running. If you want automated updates on the progress, select e.g. 5 seconds for Refresh page every X seconds and click Change.
Step 3: Monitor progress
The parts of your analysis should slowly be turning from orange to yellow (submitted -> queued), to blue (busy calculating / uploading results) to green (done). You can hover over the little cubes to view a more detailed message.
When everything is done (all green / 3's displayed), click the link to 'yeast_qtl' in the Output column. This should take you to the data matrix where the resulting QTL profiles are stored. From here, please continue to the next part of the tutorial.
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