wiki:CoverageAnalysisPipeline

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    Coverage Analysis Pipeline

    Antoine van Kampen, Barbera van Schaik, Silvia D Olabarriaga, Mark Santcroos, AMC

    Coverage per base

    Description: Calculates coverage per base. Creates a text file which you can use to make a histogram (coverage versus frequency)

    Input:

    • SortedBamFile, a sorted bam file
    • ChromSizesTxt, e.g. the chromInfo.txt from the UCSC database

    Output:

    • coverageHistogram: summary of coveragePerBase. An overview about the genome coverage of the sequence experiment. Load this into excel/calc/gnuplot/some-other-program to make a graph

    Requirements:

    Status: Implemented on grid. Source code is made available.

    Last modified 7 years ago Last modified on Oct 27, 2010 8:30:58 PM

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