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Normalize a .depth file by using average coverage of each chromosome
The utility readDepthNormalization normalizes a coverage file using its average coverage value.
Prerequisites
1) .depth file generated using findReadDepth or findFragmentDepth utility in PAVED
How
to run it?
Type java -jar PAVED.jar readDepthNormalization -h
to see list of parameters
readDepthNormalization utility takes as input a .depth file and normalizes it using average coverage value of each chromosome
Run the utility as follows:
java -jar C:\Britta\manuscript\Analysis\PAVED.jar readDepthNormalization -i C:\Britta\manuscript\Analysis\data\MNAse\normalizedData\MNAseRep2Chr5.depth
-o C:\Britta\manuscript\Analysis\data\MNAse\normalizedDataMNAseRep2Chr5Normalized.depth -j C:\Britta\manuscript\Analysis\data\MNAse\normalizedData\MNAseRep2Chr5.covPerChr
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Here, "C:\Britta\manuscript\Analysis\" is the location where the
jar file is present on the local disk, -i is the input depth file, -j is the input coverage per chromosome file generated using findAverageCoveragePerChromosome utility in PAVED and -o is the output normalized file
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