Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Viewing PET data in IGV

    I have a bed file from PET data in this format

    chr17 58754953 58754971 pair1 23 -
    chr17 58755650 58755672 pair1 25 +
    chr13 93209287 93209313 pair2 37 +
    chr13 93209438 93209457 pair2 20 -

    etc.

    I want to plot it in IGV so each pair is represented as it is in the attached figure where each read is represented as a box with a line connecting the two members of each pair. What format do I need to convert my data into? Or how can I view it this way.
    Attached Files
    Doug
    www.sharedproteomics.com

  • #2
    Nevermind. I figured it out. I made a .gff file and treated each pair like an exon from a gene.
    Doug
    www.sharedproteomics.com

    Comment


    • #3
      Hi,

      That will work, you can also use bed format but you have to use the extended form. See the UCSC site for details. BED files have the advantage of being much smaller, in general, and can also be indexed or converted to "bigBed".

      Jim

      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
      11 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
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X