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  • HG19 Genome/Exome Visualisation

    I want to visualise my Paired-End reads (.bam/.sam) files against the human HG19 genome. Does anyone know if their is a tool that is able to show the whole genome/mapped reads at once? (Preferable circular images). Or is it perhaps possible to show the mapped reads (.bam/.sam) against an whole Exome (exon regions defined in a .bed file).

    Thanks a lot

  • #2
    HG19 Genome/Exome Visualisation

    Take a look at IGV from the Broad for browsing your data.

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    • #3
      I did, but IGV did not work for me to visualise my whole genome at once. I'm only able to view small pieces at a time when zooming in.

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      • #4
        What do you want to plot across the whole genome at once? Copy number? Average coverage/megabase?

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        • #5
          Originally posted by sdavis View Post
          What do you want to plot across the whole genome at once? Copy number? Average coverage/megabase?
          I want to plot my mapped reads (.bam/.sam) against the whole hg19 genome, or whole hg19 exome (regions defined in .bed files) to see the total coverage. And I like that to have in 1 image. (example: http://www.circos.ca/images/scientif...s-epilepsy.png). But i'm not sure if there are tools like those that accept .sam/.bam/.bed.

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          • #6
            Originally posted by Puhekupla View Post
            I want to plot my mapped reads (.bam/.sam) against the whole hg19 genome, or whole hg19 exome (regions defined in .bed files) to see the total coverage. And I like that to have in 1 image. (example: http://www.circos.ca/images/scientif...s-epilepsy.png). But i'm not sure if there are tools like those that accept .sam/.bam/.bed.
            The figure in the link above is to a plot of processed data. Once you determine what you want to show, circos/rcircos could be used to plot the data. However, simply plotting all of your alignments from your BAM file (even if software existed to do so) would not be very fruitful since your BAM file probably has tens of millions of reads, making visualization of the reads impossible.

            This comes down to you having to think about what you want the plot to show first (realistically). Once you know that, you can define what tools will be best suited to the job.

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