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• Select the Aligned reads data node
• Select QA/QC from the task menu
• Select Post-alignment QA/QC from the QA/QC section of the task menu (Figure 1)

A Post-alignment QA/QC task node will be generated (Figure 2). 

• Double-click the Post-alignment QA/QC task node to view the task report

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The two graphs in the data set view (Figure 3 and Figure 4) show the alignment breakdown and coverage. Please note that the left axis label on each graph corresponds to the bars and the right axis label corresponds to the lines. 

From these graphs, we can see that more than 95% of reads were aligned, but the total number of reads for each sample varies. Normalizing for the variability in total read counts will be address in a later section of the tutorial. 

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