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weighted read display - genome browser

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  • weighted read display - genome browser

    Hi,
    does anyone know of a genome browser that collapse all exact reads to one read, but with a thickness or color that can reflect the number of reads for that loaction?
    in other words if i have a genomic location say 1-50 that has 200 reads and another location with 3-75 with 20 reads, i would like to see a longline for 1-50 location with a very thickline (or an appropriate color), while 3-75 gets a much smaller thickness? Can UCSC do this? anyother favorites you know for bed file visulaization witht this purpose?

    something like
    ___________________________
    ___________________________
    ___________________________ for 1-50


    ___________________________________ for 3-75

    thanks
    svm

  • #2
    Hi, its an interesting idea but might be difficult in practice. Would you distinguish between 10 reads, 100 reads, and 1000 reads?

    Jim

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    • #3
      yes Jim, anything approximate would be fine..like you are implying one could be on a log-scale for instance... the scale can be given to the browser in a bed file, the browser just needs to collapse and weight the "number of reads" given to it (the number could be log of the actual reads) .. i am happy to play around with the scale, i just need a browser with that feature.

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      • #4
        Hi, can you expound on what new information you would glean from such a view that you don't already get in a coverage plot? There is a little extra information there, but is not clear what would be important.

        Also, how do you define an identical read, same bases or just same position?

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        • #5
          Would wiggle plots be appropriate for your uses? They are at least supported by GBrowse (and likely other programs):

          http://genome.ucsc.edu/goldenPath/help/wiggle.html

          Here's an example of GBrowse use, where the density is used to change the colour (rather than the thickness) of the line:

          http://gmod.org/wiki/GBrowse/Uploading_Wiggle_Tracks
          Last edited by gringer; 11-04-2011, 01:12 PM. Reason: added GBrowse example

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