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PAVED- A Software suite for the analysis of epigenome-derived next generation sequencing data

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ANALYTICAL PIPELINE

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SYSTEM REQUIREMENTS

PAVED Package

Example Data

Find average coverage per chromosome

The utility findAverageCoveragePerChromosome finds average coverage value for each chromosome

Prerequisites

1) .depth file generated using findReadDepth or findFragmentDepth utility in PAVED

How to run it?

Type java -jar PAVED.jar findAverageCoveragePerChromosome -h to see list of parameters

findAverageCoveragePerChromosome utility takes as input a .depth file and finds average coverage per each chromosome

Run the utility as follows:

java -jar C:\Britta\manuscript\Analysis\PAVED.jar findAverageCoveragePerChromosome -i C:\Britta\manuscript\Analysis\data\MNAse\normalizedData\MNAseRep2Chr5.depth -o C:\Britta\manuscript\Analysis\data\MNAse\normalizedDataMNAseRep2Chr5.covPerChr

Here, "C:\Britta\manuscript\Analysis\" is the location where the jar file is present on the local disk, -i is the input depth file and -o is the output file containing average coverage per chromosome values