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

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SYSTEM REQUIREMENTS

PAVED Package  

Example Data

Averages the coverage values every x bases as specified by the user.

The utility smoothDepthFile converts a depth file to a tab file

Prerequisites

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

How to run it?

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

smoothDepthFile utility takes as input a .depth file and generates a file with values averaged over number of bases as specified by the user

Run the utility as follows:

java -jar C:\Britta\manuscript\Analysis\PAVED.jar smoothDepthFile -i C:\Britta\manuscript\Analysis\data\wholeGenome\FAIRErep2sortedNorm.depth -o C:\Britta\manuscript\Analysis\data\wholeGenome\averaged\FAIRErep2sortedNorm2000.depth -n 2000


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 smoothed depth file with values averaged over every 2000 bases