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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

Normalize Depth File

The utility normalizeDepthFile normalizes a coverage file given a numeric factor.

Prerequisites

1) Find the coverage using one of the utilities findFragmentDepth or findReadDepth

How to run it?

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

normalizeDepthFile utility takes as input a coverage file, a factor and outputs a normalized coverage file.

Run the utility as follows:
java -jar C:\Britta\manuscript\Analysis\PAVED.jar normalizeDepthFile -i C:\Britta\manuscript\Analysis\MNAse\ControlRep1Chr5.depth -o C:\Britta\manuscript\Analysis\MNAse\normalizedData\ControlRep1Chr5.depth -m 77.08907815244041

Here, "C:\Britta\manuscript\Analysis\" is the location where the jar file is present on the local disk, -i is the coverage file generated using the utility findFragmentDepth or findReadDepth, -o is the output normalized coverage file and -m is the factojava -jar C:\Britta\manuscript\Analysis\PAVED.jar normalizeDepthFile -i C:\Britta\manuscript\Analysis\MNAse\ControlRep1Chr5.depth -o C:\Britta\manuscript\Analysis\MNAse\normalizedData\ControlRep1Chr5.depth -m 77.08907815244041r.

Sample output

The sample output of the program is same as that of findFragmentDepth or findReadDepth