Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • TopHat (Tuxedo Suite) - AWS vs Local

    Hello All
    Sorry this one's a bit long
    Have come here after some testing !!

    I am trying to run Tuxedo suite for RNASeq Analysis on AWS

    Post alignment using Tophat, I have recorded significant difference in size of "accepted_hits.bam" between runs on AWS (Amazon Web Services) and Local System

    Details
    Paired end FastQs
    Size - after Adapter and quality thresholding - 7 gigs (3.5 X 2)
    Human Sample

    AWS Instance
    15 cores - of - m4.16xlarge (64 cores/256 RAM)
    Time ~45 min
    Out put accepted_hits.bam ~100mb

    Local Server
    15 cores - of - 36 cores/256 RAM
    Time ~52 min
    Out put accepted_hits.bam ~1.2GB

    Questions
    Why such significant difference? reasons?

    One thread I found, which was somewhat related


    As suggested in the above thread, I have tried running tophat, with same parameters and input files,
    on 1, 5, 10, 15, 20, 30 and 64 cores on local servers
    on 30 and 64 cores on AWS

    Interestingly, the size of "accepted_hits.bam" remained same (1.2 gb) till I reached 30 cores on local server (with specs mentioned above), and reduced (~120 mb) on 64 cores.
    On AWS, as said above, 30 and (later) 64 are giving out ~100 mb of accepted_hits.bam

    any input, suggestions and comments are welcome
    thank you for your time !!

  • #2
    Sounds like a bug to me... maybe you should try a different version of Tophat. The number of cores should not affect the size of the output bam more than a tiny amount.

    Alternatively, you could try BBMap; it's faster than Tophat and produces correct output for any number of cores

    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, 03-27-2024, 06:37 PM
    0 responses
    13 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-27-2024, 06:07 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    53 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    69 views
    0 likes
    Last Post seqadmin  
    Working...
    X