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  • problem using samtools tview viewer

    Hello,

    Has anyone had a problem using the samtools tview?

    using the command

    samtools tview sorted.bam ref.fa

    I simply get a blank black screen and no display, no error message either.

    Is this because the reference sequence is too big?
    I have not had any problems before with tview but here I am trying to view an alignment against all 5 chromosomes rather than 1 chromosome at a time.
    Any advice would be appreciated, thanks.

  • #2
    Originally posted by lindseyjane View Post
    Hello,

    Has anyone had a problem using the samtools tview?

    using the command

    samtools tview sorted.bam ref.fa

    I simply get a blank black screen and no display, no error message either.

    Is this because the reference sequence is too big?
    I have not had any problems before with tview but here I am trying to view an alignment against all 5 chromosomes rather than 1 chromosome at a time.
    Any advice would be appreciated, thanks.
    A blank screen means at that position (the start) there are no reads. Try using the "?" key to get options to move around. Specifically, use "g" to specify a "chrosition" to which you wish to move.

    Comment


    • #3
      Thank you, problem solved

      Comment


      • #4
        can you tell how to solve the problem? Because I also got the same problem, it mean that when i used the command ''samtools tview 140222A2.sorted.bam ~/tan_analysis/IRGSP-1.0_genome.fasta''

        the screening show ''NNNNNN'' all
        Can you suggest please?

        Thank you very much

        Comment

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