PAINT: Leishmania Sexual Reproductive Strategies As Resolved Through Compuational Methods Designed for Aneuploid Genomes

Jahangheer S. Shaik, Deborah E. Dobson, David L. Sacks and Stephen M. Beverleyy

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PAINT Package

Example Data

Generate a Coverage File

This page walks you though various steps required to generate an read depth(coverage) file using PAINT package.

Prerequisites

1) Align the fastq files to the reference genome of interest using your favourite aligner (Bowtie, BWA, Novoalign etc.)
2) Sort the generated Binary alignment map (BAM) file using samtools 'sort' function

How to Run it?

The findReadDepth utility of PAINT package takes a sorted bam file as input and finds coverage values at each genomic position. Type java -jar PAINT.jar findReadDepth -h for options.
The parameter -i is a sorted Binary alignment map (BAM) file as input.
The paramter -n specifies the intervals in which the read depth must be reported. If -n is set to 1, read depth at each genomic position is specified.
The paramter -o specifies the location where the output file is written.

Command Example

java -jar PAINT.jar findReadDepth -i "../DemoData/BAMS/FV1_SAT_srt.bam" -o "./DemoData/readDepth/FV1_SAT_srt.depth" -n 1

Output

The output of the listAlleles program looks as follows:

LmjF01
1       1
2       1
3       1
4       1
5       1
6       1
7       1
8       2
9       2
10      3
11      3
12      3
13      4
14      4
15      4
16      4
17      5
18      5
19      5
20      5
........

LmjF02
.........

The chromosome name is listed first followed by the coverage information.Each successive line consists of two columns. The first column specifies the base position and the second column specifies the read depth at that genomic position. If there is no coverage at a genomic position, then a "0" is reported. These values are reported until the end of the chromosome followed by the name of the next chromosome and its read depth ordered by genomic position.