Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Problems with display in IGV

    Hello everybody,
    I hope this is not off topic, I'm new in this forum.
    I have installed IGV 2.0.34 on two Windows computers, one 32bit Vista
    and another Windows7 64bit with graphics accelerator. IGV loads
    normally in both machines. I can open and see .bam files with no
    problem on the 32bit machine, but when I try to open the exact same
    files in the 64bit W7 it appears to open the file, but I can't see the
    reads or any other of the tracks. When I pass the mouse over the
    screen it gives me the read data, but I can't see the grey bars, nor
    the bases. Furthermore, the pop up read information doesn't dissapear.
    It would appear it is only a display problem, but I have tried several
    approaches but to no avail, including:
    - Checking that Java is updated.
    - Zooming in and out of the window.
    - Selecting large, medium and small genome regions.
    - Changing the screen resolution to all possible values.
    - Changing the display from 32 to 16 bit color.
    - Disabling the graphics accelerator.
    Has anyone had this problem? Any ideas on what else to try?
    Thank you very much for your help.
    Keo.

  • #2
    Hi all,
    Problem fixed.
    The IGV help team mentioned that the problem might be the reference, and I realized that my .genome file was built on the 32bit Vista machine. I just rebuilt the .genome file directly in my 64bit from the fasta of my reference instead of using the one built in the 32bit systems, and voilà, it works fine.
    Keo.

    Comment


    • #3
      Hi Keo,

      I've looked at your problem and logs a little more, and for the sake of others who might search this forum let me clarify. I think your problem stemmed from trying to move the .genome file between machines, not a 32 vs 64 bit issue. The .genome file is a zip that contains, among other things, the file path to the sequence folder. If you move it the path might not be valid anymore. This can be fixed by unzipping the .genome file (e.g. using winzip) and editing a property file, then rezipping.

      We now support indexed fastas as an alternative to the .genome file & directory. You have to load annotations separately using this option, but it is much cleaner if you anticipate moving the fasta around or sharing it. To load the fasta just use the "load genome" option (no need to import).

      Jim

      Comment


      • #4
        Thanks Jim,
        I'll keep this in mind.
        Best,
        Keo.

        Comment


        • #5
          Sure, to emphasize this only works for indexed fastas. You can index them with samtools.

          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