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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 data4HistogramDepth finds relative counts for the fold change values generated using the findReadDepth or findFragmentDepth utility of PAVED.It generates a file containing coverage values and their relative counts.

Prerequisites

Find coverage using the findReadDepth or findFragmentDepth utility of PAVED

How to run it?

Type java -jar PAVED.jar data4HistogramDepth -h to see list of parameters

data4HistogramDepth utility takes as input 1) coverage file generated using PAVED and outputs coverage values and their relative counts. It also outputs average coverage value.

Run the utility as follows:

java -jar C:\Britta\manuscript\Analysis\PAVED.jar data4HistogramDepth -i "C:\Britta\manuscript\Analysis\data\MNAse\ControlRep1Chr5.depth" -o "C:\Britta\manuscript\Analysis\data\MNAse\histogram\ControlRep1Chr5.hist"

Here, "C:\Users\jshaik\Desktop\jars\" is the location where the jar file is present on the local disk, -i is the coverage file and -o is the output file with relative counts for coverage values.

Sample output

The output consists of fold change values and their relative counts. The last line in the file reports the man coverage value and standard deviation.
histogramOfCoverage