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  • How to measure distribution of coverage across genome

    Is there a good tool for evaluating distribution of reads across genome?

    I realize there are several tools to calculate coverage in different ways, but then you usually with a large table that you still have to process. It would be nice to end up with a simple graph or a score. Seems like there should already be a nice solution to this. Is there?

  • #2
    qualimap is an easy-to-use java-prog doing this (http://qualimap.bioinfo.cipf.es/). Among other things, it generates a coverage plot (see the pictures at the bottom of the page).

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