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  • bigwig and replicates dilemma

    Hi guys!

    I am visualizing bigwig files on the genome viewer (I use IGV) from RNAseq samples of human origin.
    I have two clusters of 10 replicates each. I wanted to have just the experimental vs control track (otherwise it'll be too big screenshot, and also too confusing), but I am not sure what would be the good way to produce accurate data.

    Should I use samtools merge to combine all the replicates from group#1 and group#2 (: all experimental combined and all control combined), and use those .bam files as input to create bigwig files? Or is there any other way?

    Thanks to all!!!

    Manu

  • #2
    The ideal way to visualize this might be a box and whisker type plot using coverage values.

    5 wiggles (wig) or big wigs overlaid as plots representing (for each genomic location) the summary values for the samples as 5 wiggle lines: the 5 lines would be
    1) max, 2) min, 3) lower quartile, 4) upper quartile and 5) median for the TEST CASES.

    If you had controls, another 5 lines (in another color) could represent such CONTROLS CASES.

    Calculating it is pretty straightforward but I don't know if IGV or UCSC custom would handle it.
    Last edited by Richard Finney; 08-18-2014, 02:03 PM.

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    • #3
      It sounds messy to me to have 5 wiggles (or 10) overlaid. In my experience this is hard to interpret. I would personally just average the wiggle files and have test and control tracks separated. Its just a visualization track. The more meaningful statistics of the expression will be in DE test tables and what not, not in a browser view.

      You should be able to use wig.math from here (https://github.com/timpalpant/java-genomics-io) to do that averaging.

      Comment


      • #4
        Originally posted by Wallysb01 View Post
        It sounds messy to me to have 5 wiggles (or 10) overlaid. In my experience this is hard to interpret. I would personally just average the wiggle files and have test and control tracks separated. Its just a visualization track. The more meaningful statistics of the expression will be in DE test tables and what not, not in a browser view.

        You should be able to use wig.math from here (https://github.com/timpalpant/java-genomics-io) to do that averaging.

        Hi Wallysb01 and Richard,

        thanks for your reply!
        I agree that it is just a visualization tool...but some of the recent papers I have read on similar topics include a table with the genome browser screenshot of some DE genes. Although it's not a validation of DE - you also need to do qPCRs of course- it might be a nice thing to add to your paper.
        What do you think about that?

        thanks indeed for the advices, I will try wig.math!

        Manu

        Comment


        • #5
          Hi, good question!

          I have only 2x2 samples, but ran into the same "problem". 4 tracks seperated or overlayed do not give a nice picture. And thats what you want to have. As already mentioned, its only for visualization of the statistical correct, abstract table data.

          I use IGB and used the build in graph options, which can create an averaged multigraph from selected graphs. I used my normalized wig files for this and overlayed the 2 resulting tracks.

          Comment

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