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

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INDEX

ANALYTICAL PIPELINE

CONTACT

SYSTEM REQUIREMENTS

PAVED Package

Example Data

Track and Rest

The utility trackNRest finds the average fold change within the regions specified in the bed file and rest of the regions.

Prerequisites

1) Find the fold change using the utility foldChangeReadDepth.
2) Find peaks or valleys using the utilities findValleys and findPeaks

How to run it?

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

trackNRest utility takes as input two parameters 1) fold change file in wiggle format and 2) region(s) of interest in .bed format

Run the utility as follows:

java -jar C:\Britta\manuscript\AnalysisPAVED.jar trackNRest -i "C:\Britta\manuscript\Analysis\data\FAIRE\normalizedData\FaireRepvsInput.wig" -j "C:\Britta\manuscript\Analysis\data\FAIRE\normalizedData\FaireRepvsInput.peaks"

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 -j is the bed file containing regions of interest.

Sample output

The sample output is as follows: (type PAVED.jar instead of PeakAndValleyDetector.jar)

tracknrest

In the demo data, the fold change in the regions of interest is 8.04 and the rest of the regions have fold change of 1.79