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

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PAVED Package  

Example Data

Convert a depth file to a wiggle file

The utility convertDepth2Wiggle converts a depth file to a wiggle file

Prerequisites

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

How to run it?

Type java -jar PAVED.jar convertDepth2Wiggle -h to see list of parameters

convertDepth2Wiggle utility takes as input a .depth file and converts it into a .wiggle file

Run the utility as follows:

java -jar C:\Britta\manuscript\Analysis\PAVED.jar convertDepth2Wiggle -i C:\Britta\manuscript\Analysis\data\MNAse\normalizedData\MNAseRep2Chr5.depth -o C:\Britta\manuscript\Analysis\data\MNAse\normalizedDataMNAseRep2Chr5.wig


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 wiggle file