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Exercise I – ReadQC

  1. Navigate to Sushi Demo Server: http://fgcz-sushi-demo.uzh.ch
  2. Enter your project ID in the field: e.g. 1001, 1002 etc. alt text
  3. Select „DataSet“ to get a listing of existing DataSets in your Project. There should be only one dataset which contains the meta-information of the raw data: alt text
  4. Click on the name of this dataset to see the details, to list all Apps and to select FastqcApp alt text
  5. Keep default options and continue with ‚Next’: alt text
  6. Start the actual job with ‚Submit’: alt text
  7. Go back to main page via ‚Today’s Menu’: alt text
  8. Repeat Step3 and explore the new dataSet ‚Fastqc_....’ . After 1-3 minutes a link to the FastQC-report should be available. Select this link to open the report alt text
  9. Explore the FastQC-Report alt text
  10. Questions:

Quantity:

  • Are there under/overrepresented libraries?

Quality:

  • Are there differences in quality scores across all bases?

  • Was an adapter contamination detected? Are there differences across the libraries?

  • Do you see a relationship between GC-content and adapter content/primer dimers?

→ What could be a good preprocessing strategy for our data?