Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Read length

    Hi everyone,

    I am still new to the next gen world. I have a question about read length. I am working with nextera custom enrichment, so our product is from 300 to 1000. I am still a little confused on how the cycling occurs. We are doing 150bp paired end sequencing, so what happens to the 1000bp sequences when it goes through 150 cycles? Is 700bps or so just not read? I hope this makes sense. I am just confused on how you perform say 150bp sequencing, but not exactly 150bp is in between the adapters.

    Thanks in advance.

  • #2
    You are correct, despite your confusion! You can have fragments of many sizes. Say there is a 500 bp fragment, and the run is paired-end 100 bp reads. You'll get 100 bp of the left end of the fragment, and 100 bp of the right end of the fragment, and 300 bp of unknown sequence between. If the fragment is 100 bp, you read the same DNA twice, in different directions.

    The sequencing starts with a primer hybridizing to the adapter of your template. One nucleotide is added at a time, visualized for incorporation, and the process is repeated for the number of cycles desired (100 bp, 150 bp, etc.).
    Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

    Comment


    • #3
      Thanks a lot!

      Comment


      • #4
        Another small point is that the piece in between your two 100bp reads is unknown, but we know the two 100bp pieces should align 'somewhere' together. So finding that 'somewhere' is more accurate based on this, resulting in less wasted sequence following alignment.

        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