Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • mate pair insert size variation and de novo assembly

    Hi All

    One of my lab bench colleagues is working on a constructing an Illumina mate pair library intended for use in a target capture procedure where a substantial amount of DNA is needed. Unfortunately, if she does size selection on this library she loses 90+% of her library and so she is wondering what the consequences of not doing the size selection will have on de novo assembly using this library. I believe she is attempting to make a 6kb insert library but but the size of the fragments varies from ~3-10kb. I would probably try to assemble this data (with short insert paired end data as well) using velvet but don't have much experience with mate pair libraries. Can anyone comment as to how detrimental this level of insert size variation would be in a velvet assembly or make suggestions how to deal with it?

    Thanks

    Mark

  • #2
    That fragment range doesn't sound too bad. Even AFTER the protocol, I see size ranges that wide, and successfully assembled them.

    Comment


    • #3
      After a certain point you just won't care how many Ns are in gaps. So if you're scaffolding to a mean of 5000 bp insert, you might be wrong by 2kbp, but do you care?

      Unless you have the intention of ever filling such large gaps, this really shouldn't matter for you. And if you do try to fill them, you'll be using tools that understand you might have +/- 50% error in the lengths gaps of that size, and thus they will rely on data from other sources to fix it.

      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
      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