Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • ViralFusionSeq Confusion

    Hello everyone,

    I am trying to using ViralFusionSeq to discover viral integration events in various types of sequencing data (both RNA and DNA-seq). I have successfully gotten the program and all of its dependencies installed and configured, but am running into some difficulty in adapting it from the example data to function with our own. Specifically, I'm a bit at a loss when it comes to the Clipped Sequence and Mapped Sequence keywords, and the Viral ORF's for the RP method. The trouble is that I am hoping to run the program against a full viral database rather than against a single viral sequence. I had initially hoped the change would be as simple as removing these sections from the config file, but this causes the program to fail outright as soon as it reaches the Clipped Seq module.

    In short, is there a way to get VFS to search through a database automatically rather than having to explicitly pass each virus of interest as a parameter (not feasible when talking about thousands to hundreds of thousands of viruses)? Any assistance or advice would be greatly appreciated.

    Sincerely,
    Jason Kost

  • #2
    Hi Jason,

    Thanks for your interest in using ViralFusionSeq and I apologize that you could not run stock VFS against a whole virus database.

    I am currently occupied in other projects so I could not modify the sourcecode in person. In your situtation, I would suggest writing a script to map your reads onto your viral database and extract those Reference_name you would like to analyze and input those as keywords. Having said that, you might remove those specific keywords from the example config files and leave "virus" there, which should works.
    Marco

    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