Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Tophat2 returns empty junction file: Warning: junction database is empty!

    I am using Tophat2 V2.0.7 with this command:
    Code:
    tophat2 -p 1 --library-type fr-unstranded --segment-length 12 /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome Galaxy164-\[FASTQ_Groomer_on_data_152\].fastqsanger
    #Running:
    Code:
    [2013-02-14 03:31:11] Beginning TopHat run (v2.0.7)
    -----------------------------------------------
    [2013-02-14 03:31:11] Checking for Bowtie
    		  Bowtie version:	 2.0.6.0
    [2013-02-14 03:31:11] Checking for Samtools
    		Samtools version:	 0.1.18.0
    [2013-02-14 03:31:11] Checking for Bowtie index files
    [2013-02-14 03:31:11] Checking for reference FASTA file
    	Warning: Could not find FASTA file /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa
    [2013-02-14 03:31:11] Reconstituting reference FASTA file from Bowtie index
      Executing: /usr/bin/bowtie2-inspect /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome > ./tophat_out/tmp/genome.fa
    [2013-02-14 03:33:21] Generating SAM header for /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome
    	format:		 fastq
    	quality scale:	 phred33 (default)
    [2013-02-14 03:33:54] Preparing reads
    	 left reads: min. length=36, max. length=36, 2 kept reads (0 discarded)
    [2013-02-14 03:33:54] Mapping left_kept_reads to genome genome with Bowtie2 
    [2013-02-14 03:34:26] Mapping left_kept_reads_seg1 to genome genome with Bowtie2 (1/3)
    [2013-02-14 03:34:59] Mapping left_kept_reads_seg2 to genome genome with Bowtie2 (2/3)
    [2013-02-14 03:35:32] Mapping left_kept_reads_seg3 to genome genome with Bowtie2 (3/3)
    [2013-02-14 03:36:05] Searching for junctions via segment mapping
    Warning: junction database is empty!
    [2013-02-14 03:37:27] Reporting output tracks
    -----------------------------------------------
    [2013-02-14 03:38:48] Run complete: 00:07:37 elapsed
    The only thing I get ouput in junctions.bed is:
    Code:
    track name=junctions description="TopHat junctions"
    What am I doing wrong?

  • #2
    It seems that you only have 2 reads in your dataset (2 kept reads). I would try a bigger set of reads to start with.

    Comment


    • #3
      I tried with all the possible data but am getting the same error about junction. Is it because of the reference genome?

      Comment


      • #4
        Have you checked if the created reference fasta file wasn't empty? Mayby you could try to recreate the reference file upon analysis using bowtie2-inspect?

        Comment


        • #5
          I already have .fa file in Bowtie2Index directory and it's not empty:

          These are files with reference gnome:

          genome.1.bt2 genome.2.bt2 genome.4.bt2 genome.fa.fai genome.rev.2.bt2 reads_2.fq
          genome.3.bt2 genome.fa genome.rev.1.bt2 reads_1.fq
          Last edited by sachitad; 02-15-2013, 01:45 AM.

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Current Approaches to Protein Sequencing
            by seqadmin


            Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
            04-04-2024, 04:25 PM
          • 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

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 04-11-2024, 12:08 PM
          0 responses
          32 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 10:19 PM
          0 responses
          37 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 09:21 AM
          0 responses
          31 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-04-2024, 09:00 AM
          0 responses
          53 views
          0 likes
          Last Post seqadmin  
          Working...
          X