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

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ANALYTICAL PIPELINE

CONTACT

SYSTEM REQUIREMENTS

PAVED Package  

Example Data

Data for Histogram

The utility data4Histogram finds relative counts for the fold change values generated using the foldChangeReadDepth  utility. These counts indicate number of bases with that fold change value.

Prerequisites

1) Find the fold change using the utility  foldChangeReadDepth.

How to run it?

Type java -jar PAVED.jar data4Histogram -h to see list of parameters

data4Histogram utility takes as input  1) fold change file in wiggle format and outputs  fold changes and their relative counts

Run the utility as follows:

java -jar C:\Britta\manuscript\Analysis\PAVED.jar data4Histogram -i "C:\Britta\manuscript\Analysis\data\FAIRE\normalizedData\FaireRepvsInput.wig" -o "C:\Britta\manuscript\Analysis\data\FAIRE\normalizedData\FaireRepvsInput.hist"


Here, "C:\Britta\manuscript\Analysis\" is the location where the jar file is present on the local disk, -i is the fold change wiggle file and -o is the output file with relative counts for fold change values.

Sample output

histOP