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

Find Fragment Depth

The findFragmentDepth utility takes a bam file and finds coverage at each base based on the fragments. Each fragment is assumed to cover the region ranging from the begining of the read on the left to the end of the paired read on the right including the segment between the reads not covered by insert size. If you are dealing with single ended reads, findReadDepth utility is more appropriate.

Prerequisites

1) Filter the sorted BAM file to include only those fragments which are within in a certain insert size using the utility filterBAMbyInsertSize

How to run it?

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

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, -o is the output file containing the depth values and -s is the interval at which the fragment depth is reported. -s 1 would indicate that fragment depth is to be reported at every genomic position. If at any genomic position, there is no coverage, a 0 is reported.

Sample output

The sample output of the program is as follows:

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.