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  • Bam file visualization through console

    Hello!

    The linux server where i working on, hasn't any graphical interface, and i would like to ask, if there is any tool that visualize .bam files through console.

    Thank you.

  • #2
    samtools tview

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    • #3
      Thank you!

      Comment


      • #4
        Does it have X11? So you could use that to export graphical output to your local desktop.

        Comment


        • #5
          NO it doesn't have X11. Also when i m trying to use the samtools tview returns me that error


          [bam_index_load] fail to load BAM index.
          Cannot read index for 'accepted_hits.bam'

          Comment


          • #6
            Just index the file then (samtools index). You'll need to sort it (samtools sort) if that wasn't already done.

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            • #7
              I sorted them, indexed them and when i tried to run tview with .sort.bam file and genome.fa, it returned a huge line only with NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNs.

              Any idea ?

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              • #8
                What are the parameters you used?

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                • #9
                  Results are from tophat2.

                  Code:
                  samtools sort accepted_hints.bam accepted_hints.sort
                  samtools index accepted_hints.sort.bam 
                  samtools tview accepted_hints.sort.bam pathtogenome.fa

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                  • #10
                    You probably want to use the -p option with a position. By default, you start at base 1 of the first contig/chromosome. If there are no alignments there, then you won't see anything except whatever the reference sequence is (if this is for a mammal, then typically a bunch of Ns).

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                    • #11
                      Ok. Thank you. Seems to work.

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