Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • MiSeq intermittent blurry images.

    Here is a quality plot of our ongoing MiSeq validation run:



    Overall pretty good. But, if you look at one of the more poorly performing tiles you see:



    Seems largely to be a tile-specific issue:



    Any ideas what is causing this? Vibration seems unlikely because I would expect intermittent vibrations to effect the tiles randomly.

    --
    Phillip

  • #2
    I would guess that your stage tilt is out of spec or very close. Pretty quick fix for an FSE and tech support will replace the reagents. We had this problem on a couple of ours but after a secondary checkup they've been fine.

    Whenever we see "swirly" images like this, that was the cause.

    Comment


    • #3
      Originally posted by ECO View Post
      I would guess that your stage tilt is out of spec or very close. Pretty quick fix for an FSE and tech support will replace the reagents. We had this problem on a couple of ours but after a secondary checkup they've been fine.

      Whenever we see "swirly" images like this, that was the cause.
      Thanks. Actually the FAS did the install. I'll mention this to her. (It was just the phiX validation run, so we are not out any reagents.)

      Phillip

      Comment


      • #4
        I know...same with ours...the cluster density and other metrics may still pass their specs even with some of the image out of focus. The FAS/FSE had to come back and readjust the stage post install.

        Comment


        • #5
          Originally posted by ECO View Post
          I would guess that your stage tilt is out of spec or very close. Pretty quick fix for an FSE and tech support will replace the reagents. We had this problem on a couple of ours but after a secondary checkup they've been fine.

          Whenever we see "swirly" images like this, that was the cause.
          Wow, you are good. FAS ran a check and stage tilt failed! It had passed during the install, but somehow got out of alignment. Should be fixed now.

          We did a 2x25 nt run a couple of days back with the stage tilt presumably out of alignment -- worked fine. Could see no trace of this issue. Probably not that far off spec. Spec is -400 to 400 and the tilt was in the 700s when checked yesterday before it was re-aligned.

          Actually my FAS wants to contact your FAS/FSE to find out if there is someway to lock that alignment down. But maybe it just happens sometimes during instrument "burn in"...

          --
          Phillip

          Comment


          • #6
            Originally posted by pmiguel View Post
            Actually my FAS wants to contact your FAS/FSE to find out if there is someway to lock that alignment down. But maybe it just happens sometimes during instrument "burn in"...
            Marc Rosoff is our guy.

            Seems to be starting to happen on the second of our newest instruments as well...I'm hoping something is just loose from initial assembly and not something that will continually go out of spec.

            Saddest part is that even when our runs start to drop to <70% cluster PF because of this problem, the instrument still produces enough in-spec data that ILMN won't replace the reagents.

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Strategies for Sequencing Challenging Samples
              by seqadmin


              Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
              03-22-2024, 06:39 AM
            • seqadmin
              Techniques and Challenges in Conservation Genomics
              by seqadmin



              The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

              Avian Conservation
              Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
              03-08-2024, 10:41 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, Yesterday, 06:37 PM
            0 responses
            12 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, Yesterday, 06:07 PM
            0 responses
            10 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-22-2024, 10:03 AM
            0 responses
            52 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-21-2024, 07:32 AM
            0 responses
            68 views
            0 likes
            Last Post seqadmin  
            Working...
            X