Review unaligned reads

To determine the quality of the sequencing run, you can review the quality metrics for the unaligned reads. Primary pipeline processing, base calling, and signal processing generate these metrics. The quality metrics for unaligned reads are divided into three categories:

  • Quality of chip loading, expressed as the density of Ion Sphere™ Particles (ISPs) loaded onto the chip.

  • Quality of the ISPs that are loaded onto the chip.

  • The length of sequencing reads.

  1. In the Data tab, in the Completed Runs & Reports screen, find the report that you want to review, then click the report name link in the Report Name column.
  2. In the left navigation menu, click Unaligned Reads.
  3. Review the unaligned read quality metrics in ISP Density, ISP Summary, and Read Length panes.
  4. (Optional) Click to view more details about the information in each pane.
Related Topics
Parent topic: Open a run report
Child Topics
Run report metrics before alignment