Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Finding Indel's and long inversions in GA data

    Hi All

    I am looking for tools to find indel in GA data (short and long) and also look for large inversions after de novo assembly and comparing to reference genome.

    In the past I have used VarScan and samtools for finding indel but just wondering if people are using other software for finding indels and ways in which large inversion could be detected.


    PS: I have looked at the software wiki but would like to try tools based on your experience.

    Thanks!
    -Abhi

  • #2
    Hi,

    We haven't got into this massively as we only have 36 bp single end reads from bacteria.
    However initial results have been disappointing. We used Shrimp1 for alignment and attempted to verify 3 small <5bp indels in the wetlab. All failed, despite having 10+ reads predicting their presence.

    We tried to verify another 8 by Sanger sequencing. It turns out the sequencing was poor, and these are associated with tricky repeat rich bacterial regions.

    It seems the aligners are having some trouble with indels.

    What has your experience been like ?

    Comment


    • #3
      Hey Collindaven

      Thanks for sharing your insight. I unfortunately work only on the informatics side only and till now haven't heard back from the team for whom we did the insilico indel analysis in the past. So I dont know the false positive rate.

      What I hear and read from papers that people are finding it more useful to do indel analysis with paired end data as it gives more room to find long indels based on the known evidence of the expected distance where the read 1/2 should map.

      Thanks!
      -Abhi

      Comment


      • #4
        Hey Guys

        Just pushing this once more. I would appreciate if you could share some insight on finding long/short indel in GA data and also detecting long inversions.

        Thanks
        -Abhi

        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