Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Tophat2 can't find Bowtie2

    Hi Everyone,

    After my previous installed tophat/bowtie versions worked without a problem, I wanted to update to the newest versions and also installed tophat2 and bowtie2. Both programs have links to them from the /bin directory which is in the path.
    When trying to run the running example, tophat2 claims I do not have the correct version of bowtie installed. I'm a UNIX newbie and would appreciate any help and ideas!

    Thanks!

    Code:
    [galaxy01@gene3 test_data]$ 
    [galaxy01@gene3 test_data]$ bowtie --version
    bowtie version 0.12.5
    64-bit
    Built on sycamore.umiacs.umd.edu
    Sat Apr 24 15:56:29 EDT 2010
    Compiler: gcc version 4.1.2 20080704 (Red Hat 4.1.2-46)
    Options: -O3 -m64  -Wl,--hash-style=both
    Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
    [galaxy01@gene3 test_data]$ 
    [galaxy01@gene3 test_data]$ 
    [galaxy01@gene3 test_data]$ bowtie2 --version
    /bin/bowtie2-align version 2.1.0
    64-bit
    Built on igm3
    Thu Feb 21 09:33:38 EST 2013
    Compiler: gcc version 4.5.4 (GCC) 
    Options: -O3 -m64 -msse2 -funroll-loops -g3 
    Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
    [galaxy01@gene3 test_data]$ 
    [galaxy01@gene3 test_data]$ 
    [galaxy01@gene3 test_data]$ tophat2 --version
    TopHat v2.0.7
    [galaxy01@gene3 test_data]$ 
    [galaxy01@gene3 test_data]$ 
    [galaxy01@gene3 test_data]$ tophat2 test_ref reads_1.fq reads_2.fq
    
    [2013-02-26 09:35:20] Beginning TopHat run (v2.0.7)
    -----------------------------------------------
    [2013-02-26 09:35:20] Checking for Bowtie
    Error: TopHat requires Bowtie 2.0.5 or later
    [galaxy01@gene3 test_data]$

  • #2
    Can you unlink (or rename) bowtie (v.1) in /bin temporarily to see if that allows TopHat to recognize the correct version it needs?

    Comment


    • #3
      I'll try that but it's not a permanent solution as I want to be able to keep the previous version for other users.
      Can't I have both bowtie and bowtie2 installed side by side?

      Comment


      • #4
        Just saw this over at the TopHat site. Perhaps upgrading to latest Tophat may fix your problem.

        Version 2.0.8 is a quick fix release addressing the following issues:

        This version correctly handles the newest version of Bowtie2 v2.1.0.
        The segment mapping slow-down introduced by some Bowtie2 parameter changes in version 2.0.7 is now corrected
        There is also a new version of bowtie2 (v.2.1.0) available as well.
        Last edited by GenoMax; 02-26-2013, 12:30 PM.

        Comment


        • #5
          Originally posted by GenoMax View Post
          Just saw this over at the TopHat site. Perhaps upgrading to latest Tophat may fix your problem.
          Thanks!
          It wasn't on the site a couple of hours ago. I'll install the new tophat version and see if it helps.

          Comment


          • #6
            Updating Tophat from 2.0.7 to 2.0.8 solved the problem.

            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
            10 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, Yesterday, 06:07 PM
            0 responses
            9 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
            67 views
            0 likes
            Last Post seqadmin  
            Working...
            X