Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Anyone know how Snowshoes-FTD finds junction-spanning reads?

    Hi,

    I am trying to figure out how the gene fusion program Snowshoes-FTD finds junction spanning reads. I have the article from NAR, but it does not mention how this is done. In Figure 1, it simply states that it aligns the not-mapped reads (not mapped with BWA to either genome or their special exon-exon junction DB) to both fusion partners.

    This seems to be the most important part of a gene fusion procedure, since this will actually get you the breakpoint, but the paper does not seem to discuss at all how it does this. I assume some dynamic programming algorithm, but I can't tell.

    I don't have access to the program, since it is not freely available so maybe someone here knows?

    Thanks

    Thon
    Thon
    __________________________________
    Thon de Boer, Ph.D.
    Director of Product Management, Software
    Strand Life Sciences
    548 Market Street, Suite 82804
    San Francisco, CA 94104, USA
    [email protected]
    www.strandls.com
    Pioneers in Discovery Research Informatics
    _______________________________________

  • #2
    First,
    It used discordant paired-end to find fusion candidates.
    Example: |---geneA---|----------------------|---geneB---|

    Second,
    All unmapped reads from genome and exon-exon boundary will use megablast to align geneA and geneB to find exact break point span within geneA and geneB

    Comment


    • #3
      wonderful explaination.Thanks guy from Taipei.

      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
      66 views
      0 likes
      Last Post seqadmin  
      Working...
      X