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

Find the Number of Aligned Reads

The utility findAlignedReads takes as input a BAM file and finds the total number of reads that are aligned to the genome.

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.
3) Any file in BAM format such as the output from the utility filterBAMInsertSize may also be used as input to this program

How to run it?

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

findAlignedReads utility takes as input a sorted bam file and outputs number of reads aligned to the genome.

Run the utility as follows:

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

Sample output

The sample output is as follows: The numbe of reads that are mapped to the genome are 49149