--- title: What Should I Do If My MiSeq Fails to Measure Flow Rate When Starting Runs? description: Obviously, it's imperative that you have a good flow through your newly loaded flow cells, but what do you do when your MiSeq won't measure the flow rate? image: https://blog.seqgen.com/hubfs/social-suggested-images/Miseq-1.png --- - [MARKETPLACE](https://seqgen.com/marketplace/) - [CAREERS](https://seqgen.com/careers/) - [TERMS & CONDITIONS](https://seqgen.com/wp-content/uploads/2026/03/POL_011-Rev.A_Terms-and-Conditions-of-Sales-for-Products-and-Services.pdf) - [ISO 9001 CERTIFICATE](https://seqgen.com/wp-content/uploads/2026/01/SeqGen-Final-Cert_2026-2029.pdf) - [SALES INQUIRY](https://seqgen.com/sales-inquiry/) - [SERVICE REQUEST](http://seqgen.com/service-request/) - [TESTIMONIALS](https://seqgen.com/testimonials/) [![SeqGen](https://seqgen.com/wp-content/uploads/2020/03/seqgen_logo.png)](https://seqgen.com/) - [SeqMo Rewards](https://seqgen.com/seqmo-rewards/) - [HOME](https://seqgen.com/) - [ABOUT US](https://seqgen.com/about-us/) - [Our History](https://seqgen.com/about-us/our-history-2/) - [Our Engineers](https://seqgen.com/about-us/our-engineers/) - INSTRUMENT MODEL - [LC/MS](https://seqgen.com/instrument-model/lc-ms/) - [Sciex 3000 system](https://seqgen.com/instrument-model/lc-ms/api-3000/) - [Sciex 3200 system](https://seqgen.com/instrument-model/lc-ms/api-3200/) - [Sciex 4000 system](https://seqgen.com/instrument-model/lc-ms/api-4000/) - [Sciex 4500 system](https://seqgen.com/instrument-model/lc-ms/api-4500/) - [Sciex 5500 system](https://seqgen.com/instrument-model/lc-ms/api-5500/) - [Sciex 6500 system](https://seqgen.com/instrument-model/lc-ms/api-6500/) - [LC systems](https://seqgen.com/instrument-model/lc-ms/lc-systems/) - [DNA Analyzer](https://seqgen.com/instrument-model/dna-analyzer/) - [ABI 3100](https://seqgen.com/instrument-model/dna-analyzer/abi-3100/) - [ABI 3130/3130XL](https://seqgen.com/instrument-model/dna-analyzer/abi-3130-3130xl/) - [ABI 3500/3500XL](https://seqgen.com/instrument-model/dna-analyzer/abi-3500-3500xl/) - [ABI 3730/3730XL](https://seqgen.com/instrument-model/dna-analyzer/abi-3730-3500xl/) - [Real-Time PCR](https://seqgen.com/instrument-model/real-time-pcr/) - [ABI 7300/7500](https://seqgen.com/instrument-model/real-time-pcr/abi-7300-7500/) - [ABI 7900](https://seqgen.com/instrument-model/real-time-pcr/abi-7900/) - [Thermal Cyclers](https://seqgen.com/instrument-model/thermal-cyclers/) - [ABI 2720](https://seqgen.com/instrument-model/thermal-cyclers/abi-2720-2/) - [ABI 9700](https://seqgen.com/instrument-model/thermal-cyclers/abi-9700/) - [ABI 9800](https://seqgen.com/instrument-model/thermal-cyclers/abi-9800/) - [Liquid Handler](https://seqgen.com/instrument-model/liquid-handler/) - [Tecan Freedom Evo](https://seqgen.com/instrument-model/liquid-handler/tecan-freedom-evo/) - [Microplate Reader](https://seqgen.com/instrument-model/microplate-reader/) - [Coming Soon](https://seqgen.com/instrument-models/microplate-reader/) - [SALES](https://seqgen.com/sales/) - [SERVICE](https://seqgen.com/service/) - [CONTACT](https://seqgen.com/contact/) - [BLOG](https://blog.seqgen.com) - [HOME](http://seqgen.com/) - [ABOUT US](https://seqgen.com/about-us/) - [Our History](https://seqgen.com/about-us/our-history-2/) - [Our Engineers](https://seqgen.com/about-us/our-engineers/) - INSTRUMENT MODEL - [LC/MS](https://seqgen.com/instrument-model/lc-ms/) - [Sciex 3000 system](https://seqgen.com/instrument-model/lc-ms/api-3000/) - [Sciex 3200 system](https://seqgen.com/instrument-model/lc-ms/api-3200/) - [Sciex 4000 system](https://seqgen.com/instrument-model/lc-ms/api-4000/) - [Sciex 4500 system](https://seqgen.com/instrument-model/lc-ms/api-4500/) - [Sciex 5500 system](https://seqgen.com/instrument-model/lc-ms/api-5500/) - [Sciex 6500 system](https://seqgen.com/instrument-model/lc-ms/api-6500/) - [DNA ANALYZER](https://seqgen.com/instrument-model/dna-analyzer/) - [ABI 3100](https://seqgen.com/instrument-model/dna-analyzer/abi-3100/) - [ABI 3130/3130XL](https://seqgen.com/instrument-model/dna-analyzer/abi-3130-3130xl/) - [ABI 3500/3500XL](https://seqgen.com/instrument-model/dna-analyzer/abi-3500-3500xl/) - [ABI 3730/3730XL](https://seqgen.com/instrument-model/dna-analyzer/abi-3730-3500xl/) - [REAL-TIME PCR](https://seqgen.com/instrument-model/real-time-pcr/) - [ABI 7300/7500](https://seqgen.com/instrument-model/real-time-pcr/abi-7300-7500/) - [ABI 7900](https://seqgen.com/instrument-model/real-time-pcr/abi-7900/) - [THERMAL CYCLERS](https://seqgen.com/instrument-model/thermal-cyclers/) - [ABI 2720](https://seqgen.com/instrument-model/thermal-cyclers/abi-2720-2/) - [ABI 9700](https://seqgen.com/instrument-model/thermal-cyclers/abi-9700/) - [ABI 9800](https://seqgen.com/instrument-model/thermal-cyclers/abi-9800/) - [LIQUID HANDLER](https://seqgen.com/instrument-model/liquid-handler/) - [Tecan Freedom Evo](https://seqgen.com/instrument-model/liquid-handler/tecan-freedom-evo/) - [SALES](https://seqgen.com/sales/) - [SERVICE](https://seqgen.com/service/) - [CONTACT](https://seqgen.com/contact/) - [SERVICE REQUEST](https://seqgen.com/service-request/) - [SALES INQUIRY](https://seqgen.com/sales-inquiry/) - [BLOG](https://blog.seqgen.com/) - [TESTIMONIALS](https://seqgen.com/testimonials/) - [ISO 9001 CERTIFICATE](https://seqgen.com/wp-content/uploads/2026/01/SeqGen-Final-Cert_2026-2029.pdf) # What Should I Do If My MiSeq Fails to Measure Flow Rate When Starting Runs? 30 March 2017 [Archive](https://blog.seqgen.com/topic/archive) [0](https://blog.seqgen.com/what-should-i-do-if-my-miseq-fails-to-measure-flow-rate-when-starting-runs#comments-listing) ![Miseq.png](https://blog.seqgen.com/hs-fs/hubfs/social-suggested-images/Miseq.png?width=320&name=Miseq.png)We all love the MiSeq for the fast turnaround, remarkable data quality and its streamlined workflow. However, from time to time, our trusty machines will have an off day that can throw an elephant-sized wrench into your plans. From time to time, you may notice that you are unable to start your Miseq run because the pre-run flow check is failing. Obviously, it’s imperative that you have good flow through your newly loaded flow cells for the Miseq to generate proper clusters and good data quality. --- The Miseq needs to check and measure flow rate so that your equipment will know how much reagent it is pumping during the sequencing run. On the MiSeq, there are sensors that measure this flow. These sensors work by detecting the fluid in the line to make sure the correct volume is flowing through the machine. If your flow rate is off, your MiSeq will either over or under-pump reagents, negatively affecting your data quality.  ### Inspect the Flow Cell First Thankfully, if your MiSeq pre-run flow check is not passing, there are a number of easy troubleshooting steps that can be taken that often resolve the issue with no maintenance or service to the system needed.  First, open the MiSeq door and remove the flow cell. Clean the stage and flow cell using a wet lint-free wipe. It is a good idea to clean the stage even if no reagent buildup is visible.  While the flow cell is removed from the system, inspect it for any signs of damage such as chips, cracks or scratches. ![flow cell.jpg](https://blog.seqgen.com/hs-fs/hubfs/flow%20cell.jpg?width=320&name=flow%20cell.jpg) You'll also want to make sure the flow cell is clean, as a dirty flow cell will negatively affect data quality.  You can clean it using a lint-free wipe.  Return the flow cell to the stage, taking care that it is seated properly. Attempt another flow check.  If the flow check still fails, you can manually force fluid through the properly seated flow cell by taking the following steps in the MiSeq Control Software: - Select the following: Solution: PR2, Volume: 250, Aspiration Rate: 2500, Dispense Rate: 2500 - Select “Pump” - Retry the flow check ### If You Still Have Issues, Run a Power Cycle If you try all of these steps and the flow check still fails, you will want to power cycle the instrument: - To power cycle, close the MiSeq Control Software (MCS), shut down Windows, and switch off the instrument using the switch in the back of the unit - Power back on the system using the switch on the rear and open MCS - Attempt another flow check - If the flow check still fails, run a maintenance wash and try the flow check again If none of the previous troubleshooting steps were successful, record the lot number of the flow cell and try using a flow cell from another kit. For flow cells that fail to pass the flow check, you can contact the OEM to receive a replacement. It can be frustrating, but these machines do break down from time to time. To eliminate random down days and keep your lab running at maximum efficiency, [schedule a preventative maintenance visit on your MiSeq.](http://seqgen.com/contact/) One day with a SeqGen service technician can save you massive headaches down the road!   ### Written by [Susan Henry](https://blog.seqgen.com/author/susan-henry) Search this site on Google Search Google ### Subscribe to Email Updates ## [![New Call-to-action](https://hubspot-no-cache-na2-prod.s3.amazonaws.com/cta/default/1939955/32eb2ce8-8e54-4e61-ad50-57f6b9b23d18.png)](https://hubspot-cta-redirect-na2-prod.s3.amazonaws.com/cta/redirect/1939955/32eb2ce8-8e54-4e61-ad50-57f6b9b23d18)  ### Recent Posts ### Posts by Topic - [DNA Analyzer (49)](https://blog.seqgen.com/topic/dna-analyzer) - [Others (42)](https://blog.seqgen.com/topic/others) - [Crossword Puzzle (11)](https://blog.seqgen.com/topic/crossword-puzzle) - [3730 Series Genetic Analyzer (10)](https://blog.seqgen.com/topic/3730-series-genetic-analyzer) - [Tecan Freedom Evo (10)](https://blog.seqgen.com/topic/tecan-freedom-evo) - [3500 Series Genetic Analyzer (6)](https://blog.seqgen.com/topic/3500-series-genetic-analyzer) - [AI 101 (6)](https://blog.seqgen.com/topic/ai-101) - [Archive (6)](https://blog.seqgen.com/topic/archive) - [Events/News (6)](https://blog.seqgen.com/topic/events-news) - [LC-MS (5)](https://blog.seqgen.com/topic/lc-ms) - [Real-Time PCR (4)](https://blog.seqgen.com/topic/real-time-pcr) - [3130 Series Genetic Analyzer (2)](https://blog.seqgen.com/topic/3130-series-genetic-analyzer) see all ### Archives - [September 2026 (1)](https://blog.seqgen.com/archive/2026/09) - [August 2026 (1)](https://blog.seqgen.com/archive/2026/08) - [July 2026 (1)](https://blog.seqgen.com/archive/2026/07) - [June 2026 (2)](https://blog.seqgen.com/archive/2026/06) - [March 2026 (2)](https://blog.seqgen.com/archive/2026/03) - [February 2026 (2)](https://blog.seqgen.com/archive/2026/02) - [January 2026 (4)](https://blog.seqgen.com/archive/2026/01) - [December 2025 (3)](https://blog.seqgen.com/archive/2025/12) - [November 2025 (1)](https://blog.seqgen.com/archive/2025/11) - [October 2025 (4)](https://blog.seqgen.com/archive/2025/10) - [September 2025 (5)](https://blog.seqgen.com/archive/2025/09) - [August 2025 (1)](https://blog.seqgen.com/archive/2025/08) - [July 2025 (1)](https://blog.seqgen.com/archive/2025/07) - [June 2025 (2)](https://blog.seqgen.com/archive/2025/06) - [May 2025 (1)](https://blog.seqgen.com/archive/2025/05) - [April 2025 (2)](https://blog.seqgen.com/archive/2025/04) - [March 2025 (2)](https://blog.seqgen.com/archive/2025/03) - [February 2025 (2)](https://blog.seqgen.com/archive/2025/02) - [July 2023 (1)](https://blog.seqgen.com/archive/2023/07) - [May 2023 (1)](https://blog.seqgen.com/archive/2023/05) - [April 2023 (2)](https://blog.seqgen.com/archive/2023/04) - [March 2023 (3)](https://blog.seqgen.com/archive/2023/03) - [October 2022 (1)](https://blog.seqgen.com/archive/2022/10) - [September 2022 (1)](https://blog.seqgen.com/archive/2022/09) - [May 2022 (1)](https://blog.seqgen.com/archive/2022/05) - [February 2022 (3)](https://blog.seqgen.com/archive/2022/02) - [February 2021 (1)](https://blog.seqgen.com/archive/2021/02) - [March 2020 (2)](https://blog.seqgen.com/archive/2020/03) - [December 2019 (1)](https://blog.seqgen.com/archive/2019/12) - [November 2019 (1)](https://blog.seqgen.com/archive/2019/11) - [September 2019 (1)](https://blog.seqgen.com/archive/2019/09) - [June 2019 (1)](https://blog.seqgen.com/archive/2019/06) - [August 2018 (1)](https://blog.seqgen.com/archive/2018/08) - [May 2018 (1)](https://blog.seqgen.com/archive/2018/05) - [April 2018 (1)](https://blog.seqgen.com/archive/2018/04) - [March 2018 (1)](https://blog.seqgen.com/archive/2018/03) - [January 2018 (1)](https://blog.seqgen.com/archive/2018/01) - [December 2017 (1)](https://blog.seqgen.com/archive/2017/12) - [November 2017 (1)](https://blog.seqgen.com/archive/2017/11) - [October 2017 (1)](https://blog.seqgen.com/archive/2017/10) - [September 2017 (1)](https://blog.seqgen.com/archive/2017/09) - [August 2017 (2)](https://blog.seqgen.com/archive/2017/08) - [July 2017 (2)](https://blog.seqgen.com/archive/2017/07) - [June 2017 (2)](https://blog.seqgen.com/archive/2017/06) - [May 2017 (5)](https://blog.seqgen.com/archive/2017/05) - [April 2017 (1)](https://blog.seqgen.com/archive/2017/04) - [March 2017 (5)](https://blog.seqgen.com/archive/2017/03) - [February 2017 (4)](https://blog.seqgen.com/archive/2017/02) - [January 2017 (4)](https://blog.seqgen.com/archive/2017/01) - [December 2016 (3)](https://blog.seqgen.com/archive/2016/12) - [November 2016 (3)](https://blog.seqgen.com/archive/2016/11) - [October 2016 (4)](https://blog.seqgen.com/archive/2016/10) - [September 2016 (3)](https://blog.seqgen.com/archive/2016/09) - [August 2016 (5)](https://blog.seqgen.com/archive/2016/08) - [July 2016 (3)](https://blog.seqgen.com/archive/2016/07) - [June 2016 (3)](https://blog.seqgen.com/archive/2016/06) - [May 2016 (4)](https://blog.seqgen.com/archive/2016/05) - [April 2016 (4)](https://blog.seqgen.com/archive/2016/04) - [March 2016 (4)](https://blog.seqgen.com/archive/2016/03) - [February 2016 (30)](https://blog.seqgen.com/archive/2016/02) see all ## Contact Us #### SeqGen, Inc. 1725 Del Amo Blvd Torrance, CA 90501 #### +1 877 377 3743 #### +1 800 790 4830 #### [info@seqgen.com](mailto:%20info@seqgen.com) #### Opening Hours Monday - Friday: 8:30AM PST - 5:30PM PST ## Social Links - - - - SeqGen is an independently owned and operated provider of repair services and refurbished laboratory equipment. Any product names, logos, brands, and other trademarks or images featured or referred to within the SeqGen website and/or on any social media forum are the property of their respective trademark holders or OEMs. These trademark holders are not affiliated with SeqGen or its website. These trademark holders do not sponsor or endorse SeqGen or any of its products or comments. The use of any trade name or trademark is for identification and reference purposes only and does not imply any association with the trademark holder of their product brand. ```json { "@context" : "https://schema.org", "@type" : "BlogPosting", "author" : { "@type" : "Person", "name" : "Susan Henry", "url" : "https://blog.seqgen.com/author/susan-henry" }, "dateModified" : "2026-03-14T01:06:52.221Z", "datePublished" : "2017-03-30T14:33:53.000Z", "headline" : "What Should I Do If My MiSeq Fails to Measure Flow Rate When Starting Runs?", "image" : [ "https://blog.seqgen.com/hubfs/social-suggested-images/Miseq-1.png" ], "mainEntityOfPage" : { "@id" : "https://blog.seqgen.com/what-should-i-do-if-my-miseq-fails-to-measure-flow-rate-when-starting-runs", "@type" : "WebPage" }, "publisher" : { "@type" : "Organization", "logo" : { "@type" : "ImageObject", "url" : "https://blog.seqgen.com/hubfs/SmallLogo-2.png" }, "name" : "SeqGen, Inc." } } ```