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  • View BAM file

    When I see a BAM file by running the command, "samfile view -h accepted_hits.bam",
    the result is like the attachment.

    My quetion is,
    "Is it okay for the rows from Contig0 to Contig9 to have shorter space ahead of LN than the rows from Contig10 to the end do have?"

    Thank you in advance.
    Attached Files
    Last edited by syintel87; 01-05-2013, 06:16 AM.

  • #2
    That is not SPACE, but TAB.

    Comment


    • #3
      It's a column-based format separated by tabs. For visualization purposes, if you want to pipe the tab-separated columns into something that looks pretty on the screen, in Linux you can use 'column -t' like this (notice only first 100 lines):

      samfile view -h accepted_hits.bam | head -n 100 | column -s $'\t' -t | less

      Comment


      • #4
        Originally posted by avilella View Post
        It's a column-based format separated by tabs. For visualization purposes, if you want to pipe the tab-separated columns into something that looks pretty on the screen, in Linux you can use 'column -t' like this (notice only first 100 lines):

        samfile view -h accepted_hits.bam | head -n 100 | column -s $'\t' -t | less
        Oh, thank you very much!

        Comment

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