If the MiSeq fails to measure flow rate when starting a run, perform the following steps to resolve the issue. Steps 1 and 2 can be performed together, before repeating the flow check.

1. Inspect the flow cell and gasket for any signs of damage:
   1. Open the MiSeq door and remove the flow cell.
   2. Confirm that the flow cell gasket is flush as shown in the following images.
   
   
   
   3. If the gasket is raised or distorted, do not use this flow cell. Email Technical Support to recieve a replacement for the defective flow cell. Technical Support will ask for the lot and serial numbers of the affected flow cell, and may ask for a picture of the defective gasket for quality control. Proceed with the pre-run checks using a new flow cell from another kit, if available.
   4. If the gasket is flush with the plastic cartridge, clean, and reseat the flow cell.
2. Clean and reseat the flow cell:
   1. Lightly rinse the flow cell with laboratory-grade water until both the glass and plastic cartridge are thoroughly rinsed of excess salts.
   2. Using care around the black flow cell port gasket, thoroughly dry the flow cell and cartridge with a lint-free lens cleaning tissue. Gently pat dry in the area of the gasket and adjacent glass.
   3. Clean the flow cell glass with an alcohol wipe, but do not use alcohol on the gasket.
   4. Check the flow cell stage for any debris or salt and clean the flow cell stage using an alcohol wipe or a lint-free tissue moistened with ethanol.
   5. Return the flow cell to the stage, and make sure that it is seated properly.
   6. Using MiSeq Control Software, perform another flow check.
3. If the flow check still fails, power cycle the instrument:
   1. Close MiSeq Control Software, shut down Windows, and turn off the instrument using the power switch on the back panel.
   2. Leave the instrument off for at least 2 minutes, to allow all parts to completely power down.
   3. Turn on the instrument using the power switch on the back panel.
   4. Using MiSeq Control Software, perform another flow check.
4. If the flow check still fails, use a different flow cell (eg, from another kit):
   1. Open the MiSeq door and remove the flow cell.
   2. Clean the flow cell as described in step 2.
   3. Place the new flow cell on the stage, and make sure that it is seated properly.
   4. Using MiSeq Control Software, go back in the run set up to repeat the flow cell RFID check, this will record the new consumable information.
   5. Continue with the run set up and perform another flow check.
   6. If the flow check passes, record the lot number of the flow cell and email Technical Support to receive a replacement for the defective flow cell.
5. If the issue persists with a new flow cell, email Technical Support for further assistance.