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  • BAM viewer that displays by insert

    Is there a BAM viewer that allows you to display by insert rather than only by read?

    Most BAM visualization tools treat each read separately. However, for paired-end data, it can be helpful to view each insert as its own entity. I would imagine each read being a rectangle, with another glyph that either bridges the gap (probably a line) or shows the overlap (differently shaded rectangle, maybe?).

    Or, as a compromise, it could display each read as a separate entity, but highlight a read when you hover over its mate, or something like that.

    I had thought this was possible in IGV, but couldn't figure it out with the version I was using (this was awhile ago, though). My google skills have come up short on this question.

    Thanks,
    Michael

  • #2
    Have you tried the paired stacked mode in Tablet? The two reads are placed on the same row, with a dashed line between them. Mouse over one will highlight the other as well.

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    • #3
      I had never even run across Tablet. It looks quite slick, and I see the two paired-end modes. This is great, thanks!

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      • #4
        Originally posted by mcrusch View Post
        I had thought this was possible in IGV, but couldn't figure it out with the version I was using (this was awhile ago, though)
        Have you tried the current IGV yet? I think version 2.0 (May 2011) or later should show paired reads.

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        • #5
          bambino: java bam view and snp detector

          Check out bambino:



          for standalone viewer.

          online viewer with public sample data sets:


          example:
          <a href="http://imgur.com/YI1KB"><img src="http://i.imgur.com/YI1KB.png" alt="" title="Hosted by imgur.com" /></a>

          Comment

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