Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Problems with mapping SOLID color space sequences to hg19 using TopHat

    Hi,

    I got a problem when mapping SOLID short sequences to hg19 using tophat. The human UCSC hg19 color space index was downloaded from bowtie website(http://bowtie-bio.sourceforge.net/manual.shtml). The variant, $bowtieInputFile, in the following command, is the name of the fastq file. I have used the same command line, except omiting argument -C (which is specially for color space), to successfully map base space reads to hg19. But the problem, "segment-based junction search failed with err =1", always show up when doing color space mapping at the step "Searching for junctions via segment mapping".

    Do you guys have any idea how I can avoid this problem?

    Thanks in advance!

    David





    > tophat --solexa-quals -p 12 -C --output-dir tophat.output ~/Utilities/bowtie/bowtie-0.12.7/indexes/hg19_c $bowtieInputFile | tee -a fastq2bigwig.log

    [Fri Jun 24 16:11:08 2011] Beginning TopHat run (v1.3.0)
    -----------------------------------------------
    [Fri Jun 24 16:11:08 2011] Preparing output location tophat.output/
    [Fri Jun 24 16:11:08 2011] Checking for Bowtie index files
    [Fri Jun 24 16:11:08 2011] Checking for reference FASTA file
    Warning: Could not find FASTA file /home/david/Utilities/bowtie/bowtie-0.12.7/indexes/hg19_c.fa
    [Fri Jun 24 16:11:08 2011] Reconstituting reference FASTA file from Bowtie index
    Executing: /home/david/bin/bowtie-inspect /home/david/Utilities/bowtie/bowtie-0.12.7/indexes/hg19_c > tophat.output/tmp/hg19_c.fa
    [Fri Jun 24 16:13:12 2011] Checking for Bowtie
    Bowtie version: 0.12.7.0
    [Fri Jun 24 16:13:12 2011] Checking for Samtools
    Samtools Version: 0.1.16
    [Fri Jun 24 16:13:12 2011] Generating SAM header for /home/david/Utilities/bowtie/bowtie-0.12.7/indexes/hg19_c
    [Fri Jun 24 16:13:13 2011] Preparing reads
    format: fastq
    quality scale: solexa33 (reads generated with GA pipeline version < 1.3)
    Left reads: min. length=51, count=737097
    [Fri Jun 24 16:13:26 2011] Mapping left_kept_reads against hg19_c with Bowtie
    [Fri Jun 24 16:13:46 2011] Processing bowtie hits
    [Fri Jun 24 16:15:16 2011] Mapping left_kept_reads_seg1 against hg19_c with Bowtie (1/2)
    [Fri Jun 24 16:16:03 2011] Mapping left_kept_reads_seg2 against hg19_c with Bowtie (2/2)
    [Fri Jun 24 16:16:50 2011] Searching for junctions via segment mapping
    [FAILED]
    Error: segment-based junction search failed with err =1

  • #2
    had the same error. you may want to give the new version (Tophat 1.3.1) a try since there were some SOLiD specific fixes in it. if that doesn't work, i've had some luck rolling back to 1.2.0, and, more routinely, use abi's aligner.

    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
    12 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