Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • tophat / bowtie mapping discrepancies

    I am mapping 50 bp SOLiD RNA-Seq reads to the mouse genome.

    When I use bowtie, I get ~60% mapping (I am running bowtie with -e 950 as has been suggested elsewhere for mapping SOLiD runs with bowtie)

    As there was no direct way to give tophat the -e option, I changed line 872 in the tophat python script from
    Code:
    bowtie_header_cmd = [bowtie_path, "--sam"]
    to
    Code:
    bowtie_header_cmd = [bowtie_path, "--sam", "-e 950"]
    When I run tophat with this option, I still get very poor mapping, of about 25%

    Why is there this discrepancy, as one would assume that all of the unspliced mapping that bowtie does should be reproducible by tophat ?

    Vineeth

  • #2
    Hi vineeth,

    Please verify with the author(s) if your way of passing "-e 950" from Tophat to Bowtie. From the Tophat manual, it has very limited options to pass parameters to Bowtie. The manual says Tophat is currently optimized for 75bp or longer SOLID reads. I am not sure what it actually means but it might have contributed to your observation.

    Douglas

    Comment


    • #3
      That really should not be an issue as this is the pythonic way (using the subprocess module) of building a command for executing something on the command-line.
      Further when I look at the run logs in the logs folder that TopHat creates, I see the bowtie command formed without issue.

      What I am wondering is since TopHat works serially by first aligning to the genome, then taking the unmapped reads and trying to align it to the splice junction which is where the read length matters (so even if the 75 bp recommendation makes a huge difference) I should only see an increase in mapping as opposed to just using bowtie; what confounds me is why I see the mapping decrease when compared to just using bowtie

      Comment


      • #4
        Hi Vineeth,

        Conceptually you are right but I am not sure how exactly tophat implements the concept. Again, please send your request to the tophat user forum or the author for a direct answer. At the same time, you may compare the mapping rates b/t Bowtie and Tophat without the option "-e 950" to see the trend? Occasionally these logical machines do illogical things.

        Douglas

        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