Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • iSeq 100 user new here

    Hi Folks,
    iSeq 100 user here, checking in!
    May all your runs be bountiful
    Wool.

  • #2
    Hi Everyone, We acquired this machine recently. we are resource-limited researchers and want to sequence the CoV-2 genome from a limited number of patients. How many iseq cartridges will be needed per sample, if we use Enrichment Sequencing by Spiked Primer MSSPE method?

    Comment


    • #3
      Hello Everyone,
      I know this thread is quite old, but wanted to know how has your experience been so far with the iSeq 100?

      We have only performed one run, and although Q30 was quite good for the Read 1 and 2, the indexes were read with lower Q30, even though we had a good balance of bases in each cycle (checked after the run in basespace).

      I was wondering if there were other tips to improve Q30 during indexing? It's a shame to lose good reads due to poor indexing

      Comment


      • #4
        jjimenez I would imagine that the only way to improve the Q30 for index reads is to further increase the index complexity or add more PhiX. You said you had a good balance but I wondered if there was a way you further increase the diversity of these bases.

        Comment


        • #5
          Click image for larger version

Name:	Imx12.png
Views:	136
Size:	737.6 KB
ID:	324914
          OK,
          So this was not the greatest SeqRun, a lot of short fragments that give rise to the Poly-Gs you see after Cycle 120 (clearly, we have to be more stringent with the size selection). Going back to the Q30 metrics

          Read 1: 92.75% >Q30
          Read 2: 82.71% >Q30
          Read 3: 79.38% >Q30
          Read 4: 90.02% >Q30


          During the indexing reads, no base goes above 40% representantion. I wouldn't think its a diversity issue? And PhiX wouldn't help, since its not indexed (unless we get the indexed one from other sources, but I dont think we'll do that)

          The run was a bit underloaded though (82% ocupation), I wonder if that has any effect.

          Comment


          • #6
            jjimenez you're right, for some reason, I kept thinking PhiX adds to the index diversity but it doesn't. Although having a slightly underloaded run shouldn't cause this issue either. I haven't run anything on the iSeq yet, but whenever I had this problem on the NextSeq, I would just spike in other libraries for additional diversity. I know that doesn't answer your question but it seemed to help.

            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
            8 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, Yesterday, 06:07 PM
            0 responses
            8 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-22-2024, 10:03 AM
            0 responses
            49 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-21-2024, 07:32 AM
            0 responses
            67 views
            0 likes
            Last Post seqadmin  
            Working...
            X