Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Physical Coverage

    Hi everyone,
    still working on a university project.
    Now i have a doubt: i have several mate pairs with one mate (call it A) aligning once and the other one (B) aligning twice.
    If i want to calculate the physical coverage on a reference genome, do i have to consider both the matepairs i'd have joining A with both the aligning sites of B?
    Or i have to choose one between the two sites where B aligns?
    Thanks

  • #2
    The answer is "both" or "one". Depends. You ask a general question and get a general answer.

    I assume that all alignments are strong and valid, that the reference is complete, that the reference only has one A and one B, and that your mate pair library is deep enough to not skip potential pairings. In that case let us think about how such a situation can occur. The reference should look like:

    ...AAAA.....BBBB...

    And your sample looks like (where 'B1' and 'B2' are the same B-mate only numbered differently):

    case X) ...AAAA....B1B1B1...B2B2B2...
    or
    case Y) ...B2B2B2...AAAAA...B1B1B1

    Or some variant on the above. In other words region B has been duplicated without A also being duplicated. In 'case X' you would only want to count the distance between A and B2. Adding in the distance between A and B1 would add too much distance. In 'case Y' you would want to count both distances.

    If my original assumptions are not valid then there are many other cases which would explain your findings.

    Comment


    • #3
      If you know the insert size then only one of the two "B" alignment sites should be correct. If both B alignment sites are within margin of insert size variation then you would have a multi-mapper situation.

      Comment


      • #4
        Yes probably is a region who is repeated ad some matepairs have only right (or left) read aligning twice in the repeated regions.
        Well... so probably the best approach is to generate two different tracks, one with all possible mates and the other introducing a "bias" to consider valid only the mp sizes between a range (maybe mean +- 3*sigma).
        It is indeed useful to show that probabily i have one more clue about a possible repeat.
        Thanks

        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