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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

Find Read Depth

The findReadDepth utility takes a bam file and finds coverage at each base based on the reads. If you have alignments based on single end reads or want to treat each read independent of alignment of its pair, then this utility is more appropriate.

Prerequisites

1) Align the fastq files to the genome of interest using your choice of alignment algorithm (BWA, BOWTIE and Novoalign)
2) Convert to binary alignment map format and sort by using Samtools.

How to run it?

Type java -jar PAVED.jar findReadDepth -h to see the list of options

Run the utility as follows:

java -jar C:\Britta\manuscript\Analysis\PAVED.jar findReadDepth -i "C:\Britta\manuscript\Analysis\data\BAMFilesInsertSize\MNAseRep2Chr5.bam" -o "C:\Britta\manuscript\Analysis\data\MNAse\MNAseRep2Chr5.depth" -n 1

Here, "C:\Britta\manuscript\Analysis\" is the location where the jar file is present on the local disk, -i is the input sorted bam file, -o is the output file containing the depth values and -n is the interval at which the read depth is reported. -n 1 would indicate that the read depth is to be reported at every base where there is coverage.

Sample output

The sample output of the program is similar to the output of findFragmentDepth utility
fragment depth output
The chromosome name followed by coverage at bases specified by the interval are reported. For example, the base 350025 on the chromosome LmjF05 has coverage of 8.