Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Are the mate-pair reads always shadowed by their friends the paired-end (picture)

    ** Title should be "Are the mate-pair reads always shadowed by their friends the paired-end reads (picture)"

    So, are the Illumina mate-pair reads always shadowed by their friends the paired-end reads ?

    See picture -> http://imgur.com/LNwws

    In the picture above, I can see two populations:

    - 250 +/- 25
    - 2250 +/- 225

    (approximations)

    What cause these during the library preparation ?

    I thought only the 2250 +/- 225 would be fished out by the biotin/streptavidin step.


    (data are from Assemblathon 2, this is the snake dataset)


    Thanks !

    Sébastien
    Last edited by seb567; 07-14-2011, 07:01 AM. Reason: typo

  • #2
    Originally posted by seb567 View Post
    So, are the Illumina mate-pair reads always shadowed by their friends the paired-end reads ?
    In short, it seems yes.

    Originally posted by seb567 View Post
    In the picture above, I can see two populations:

    - 250 +/- 25
    - 2250 +/- 225

    (approximations)

    What cause these during the library preparation ?

    I thought only the 2250 +/- 225 would be fished out by the biotin/streptavidin step.
    Indeed - those fragments which span the splice are enriched, relative to those which come from a linear stretch of the original DNA. But the latter massively out-weigh the former (increasingly so at longer MP lengths - since there are more bad fragments, still only one good fragment), so the strep merely tilts the balance a bit in favour of the 'from the splice' fragments. The ratio can go from something like 10:1 against the spiced fragments to maybe 5:1 in favour - which isn't all that bad.

    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
    51 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