Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Fusion Hunter for Finding Fusion genes

    Hi All ,

    I am using Fusion Hunter for finding Fusion transcripts from RNA-seq data. Mine is Paired end datasets. Which is not alike to left and Right ends, but when I give it in the command line with FusionHunter

    I am getting the following Error message,
    Unexpected parameterTue Apr 1 18:53:31 2014: Checking configurations
    You should check your configuration file, L read should not be the same as R read!

    The command I used,

    ${fusionH}/FusionHunter.pl FusionHunter.cfg L=/home/USER/Rna_seq_patient_1/RE_3_L001_1.fastq; R=/home/USER/Rna_seq_patient_1/RE_3_L001_2.fastq; BowtieIdx=/home/USER/Tools/FusionHunter/FusionHunter-v1.4-Linux_x86_64/bin/refseq/AnnotationFiles_hg19/bowtie_index/hg19 Gene_annotation=/home/USER/Tools/FusionHunter/FusionHunter-v1.4-Linux_x86_64/bin/refseq/AnnotationFiles_hg19/hg19.ucscKnownGene

    It would be great if soemone could help me to knwo where I am going wrong.

    I have checked both Left and right reads which is not SAME

    Thank you
    Kind regards,
    Alva

  • #2
    Originally posted by alvarani View Post
    Hi All ,

    I am using Fusion Hunter for finding Fusion transcripts from RNA-seq data. Mine is Paired end datasets. Which is not alike to left and Right ends, but when I give it in the command line with FusionHunter

    I am getting the following Error message,
    Unexpected parameterTue Apr 1 18:53:31 2014: Checking configurations
    You should check your configuration file, L read should not be the same as R read!

    The command I used,

    ${fusionH}/FusionHunter.pl FusionHunter.cfg L=/home/USER/Rna_seq_patient_1/RE_3_L001_1.fastq; R=/home/USER/Rna_seq_patient_1/RE_3_L001_2.fastq; BowtieIdx=/home/USER/Tools/FusionHunter/FusionHunter-v1.4-Linux_x86_64/bin/refseq/AnnotationFiles_hg19/bowtie_index/hg19 Gene_annotation=/home/USER/Tools/FusionHunter/FusionHunter-v1.4-Linux_x86_64/bin/refseq/AnnotationFiles_hg19/hg19.ucscKnownGene

    It would be great if soemone could help me to knwo where I am going wrong.

    I have checked both Left and right reads which is not SAME

    Thank you
    Have you tried FusionCatcher?
    Finder of Somatic Fusion Genes in RNA-seq data. Contribute to ndaniel/fusioncatcher development by creating an account on GitHub.

    Comment


    • #3
      Thanks I have tried and its working perfectly..
      Kind regards,
      Alva

      Comment


      • #4
        Is there any way to avoid this problem in Fusion hunter? I want to compare several tools.


        Originally posted by ndaniel View Post
        Have you tried FusionCatcher?
        http://code.google.com/p/fusioncatcher/

        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
        7 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        7 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
        66 views
        0 likes
        Last Post seqadmin  
        Working...
        X