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Quality Control

FastQC tool to analyse the fastq (or fastq.gz) datasets

  1. Create a new history and name it Quality Control

  2. Copy again all fastq.gz files from the data library into this history. You should have 11 datasets in your history

  3. Select the fastqc tool.

  4. In the Short read data from your current history menu, select the multiple datasets button.

  5. Shift-Click to select all 11 datasets

  6. Click Execute

  • Look at the results of FastQC: These are the datasets named FastQC on data xx: Webpage

MultiQC to aggregate and have a general view of sequence qualities in the project

  1. Select the MultiQCtool (you can use the search bar).

  2. Which tool was used generate logs? : Select FastQC

  3. Type of FastQC output? : Select Raw data

  4. FastQC output Cmd-Click (discontinuous, multiple selection) the 11 files named FastQC on xx: RawData

  5. Click Execute

Look at the result of MultiQC, dataset named MultiQC on ...: Webpage

  • Pay attention to the General Statistics that indicate the read sizes.
  • Pay attention to the Sequence Quality Histograms. What can you say about the quality of the samples ?
  • Have a look to the Adapter Content section.