Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Low computation usage on AWS using Galaxy

    Hi Everyone,

    I am attempting to analyze HiSeq 2500 RNA-Seq data using a Galaxy instance run through AWS, but the analysis is taking an unexpectedly long time (to run around 10M reads through Tophat using XenTro2 as the reference genome has taken over 3 hours and no end is in sight.)

    Looking at the core usage on AWS monitor it appears that the Galaxy instance is only using 8% of a c3.8xlarge (with autoscaling set to allow it to use up to four c3.8xlarge if needed).

    Is this normal? Is there a way to push Tophat to use more of the computing resources available through AWS?

    Thanks

  • #2
    Are you using a prebuilt galaxy image? It is may be configured to use only one core for tophat. If you are not comfortable using command line/have good knowledge of aws it may be more trouble than it is worth to go modifying configs.

    You may want to install tophat directly in your aws instance and use that instead of galaxy.

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