Guidance for discarding a run setup after a flow cell is loaded and instrument priming is complete

If you discover an error in one of the run setup parameters after completing reagent preparation, priming, and flow cell loading steps, discard the run and restart the setup process.  

Common errors in run setup include selecting the incorrect sequencing recipe, configuring incorrect optional settings, or entering an incorrect number of cycles. 

Note: Although sequencing cartridges contain sufficient reagent for a second priming event, we do not recommend priming with a new flow cell seated. Priming over a new flow cell can reduce sequencing output and negatively impact overall performance. In contrast, performing a second prime over a used flow cell is not expected to affect sequencing performance.  

The instructions below describe how to set up a new run and skip the priming step. This approach requires an external keyboard.  

After discarding the run and returning to the main screen:  

1. Select New Run. 
2. Select Sequencing.
3. Select Cloudbreak™ or Trinity™. 
4. Select Side A, Side B, or Both.  
5. Select Manual or Planned Run.
   NOTE: If the discarded run was a Planned Run created in ElemBio Cloud™, the system removes it from the available list. You must set up the run again either manually on the instrument or by recreating it in ElemBio Cloud. 

If Manual was selected: 

1. Define the Manual Run Parameters as normal (refer to the Cloudbreak sequencing or Trinity Sequencing User Guide).  
2. After confirming all parameters are correct, connect a USB/wireless keyboard (USB ports are located on the upper rightside of the instrument and on the back near the power connection) 
3. On the keyboard, press Ctrl+Shift+S simultaneously. 
4. Select the Do not prime checkbox that appears in the lower-left corner of the screen (You may need to scroll down for this option to appear). 

If Planned Run was selected:  

1. Select the appropriate run from the list of available pre-planned runs.  
2. Select the appropriate storage location.  
3. Connect a USB/wireless keyboard (USB ports are located on the upper right- side of the instrument and on the back near the power connection). 
4. On the keyboard, press Ctrl+Shift+S together  
5. Select the Do not prime checkbox that appears in the lower-left of the screen (You may need to scroll down for this option to appear.) 

For all run plan types: 

1. Proceed through Prepare Reagents, Load Reagents, and Empty Waste, ensuring the appropriate reagents are in place and waste is discarded. Select Next to advance to the priming step.  
2. The system displays the standard priming countdown timer. This step simulates priming only and completes within approximately 30 seconds.  
3. Proceed to the Load Flow Cell step. Open the nest, reseat the same flow cell, and re-clamp it in place. Close the Nest and select Next. 
4. Review the run parameters to confirm they are correct. 
5. Start the new run.