How to Troubleshoot No Intensity or 0% Passing Filter at Inlet and Outlet Tiles on NovaSeq X/X Plus
Issues with sequencing runs presenting No Intensity or 0% Clusters Passing Filter for tiles at both the flow cell inlet and outlet are typically caused by skewed flow cell registration. The root cause for this can be either a transient flow cell seating issue, or issues with the flow cell clamping assembly.
Figure 1: 0% Intensity in Inlet and Outlet of Flow Cell Chart in Sequencing Analysis Viewer (SAV)
Figure 2. 0% Cluster Passing Filters in Inlet and Outlet of Flow Cell Chart in Sequencing Analysis Viewer (SAV)
If a NovaSeq X/X Plus sequencing run shows No Intensity or 0% Clusters Passing Filters in tiles at the flow cell inlet and outlet across all lanes, collect the following files from the instrument.