Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • test of Xgen blocking oligo

    Did someone try the XGen blocking oligo from IDT instead of classical blocking oligos ? Is there a improvement of the off target ?

  • #2
    Hi, thank you for your answer.
    I understand that you use dual indexing.
    My first question is : Did you try specific Xgen blocker or the universal one for Illumina HT libraries ?
    My second one : what was the on-target before using the Xgen blocker ? Is there an improvement by using it ?

    Comment


    • #3
      Thanks superduper,

      I'm doing to setup pre indexing hybridization method and test xGen IDT oligo blocks.
      I'm happy to meet you here.

      I am a little of bit surprised that on-target rate of perfect complementary blocking oligo was lower than xGen.

      Conceptually some idea maybe was in synthesis of oligo for blocking.

      Comment


      • #4
        Originally posted by superduper
        I was using one barcode per library.
        1. I used the universal 8nt blocking oligo (mix of TS-p5 and TS-p7(8nt))

        2. my on-targets were:
        single capture; barcoding happens after hyb step (basically XT protocol): 70%
        XGen blocking: 58-73%
        Inosines instead of barcode location: up to 33%
        perfect complement: 45%
        random nucleotides: up to 35%

        This is for PE37 sequencing. To compare samples where I had run reads longer, I clipped them back to PE37 to have a fair comparison between different conditions.
        Your % on-target will increase the longer your read lengths are; I saw PE101 of 82% translate to 69% when I clipped it to PE37.
        Did you add any kind of termination to the blocking oligo?

        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
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        9 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        51 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