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| exclude | Additional Assistance |
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After alignment has completed, we can view the quality of alignment by performing post-alignment QA/QC.
- Click the Aligned reads data node
- Click QA/QC inthe task menu
- Click Post-alignment QA/QC from the QA/QC section of the task menu (Figure 1)
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| SubtitleText | Invoking Post-alignment QA/QC |
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| AnchorName | Invoking post-alignment QA/QC |
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A Post-alignment QA/QC task node will be generated (Figure 2).
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| SubtitleText | Post-alignment QA/QC task node |
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| AnchorName | Post-alignment QA/QC task node |
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- Double-click the Post-alignment QA/QC task node to view the task report
Similar to the Pre-alignment QA/QC task report, general quality information about the whole data set is displayed and sample-level reports can be opened by clicking a sample name in the table.
The top two graphs in the data set view (Figure 3) show the alignment breakdown and coverage.
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| SubtitleText | Alignment statistics for the data set |
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| AnchorName | Alignment breakdown |
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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 addressed in a later section of the tutorial.
For more information about the graphs and information presented in the Post-alignment QA/QC task report, see the Post-alignment QA/QC user guide.