View Source

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)

Flow Documentation > Running post-alignment QA/QC > Screenshot 2023-08-09 at 14.13.39.png

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

Flow Documentation > Running post-alignment QA/QC > Screenshot 2023-08-09 at 14.20.35.png

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.

Flow Documentation > Running post-alignment QA/QC > Screenshot 2023-08-09 at 14.21.02.png

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.