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. Beverley

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SYSTEM REQUIREMENTS

PAINT Package

Example Data

Find Reads aligned to both the genomes and to respective genomes

The study of inter-species hybrids requires focusing on regions that are conserved across both the genomes. This utility finds reads common to both the genomes are reads that are specific to each genome

Prerequisites

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

How to Run it?

The FindCommonSpecificReads utility of PAINT package takes sorted bam file and finds reads common to both the genomes and those specific to individual genomes respectively. Type java -jar PAINT.jar FindCommonSpecificReads -h for options.

-i is the BAM file from species 1 generated by aligning fastq reads to a reference genome of species 1 (or something close to it)
-j is the BAM file from species 2 generated by aligning fastq reads to a reference genome of species 2 (or something close to it)
-o is the output directory where three files are written. The files with "_specific" suffix contain the reads that are specific to each genome. The file with "Comm" suffix contains reads that aligned to both the genomes. These reads are indicative of regions that are conserved across both the genomes. Since two reference genomes are involved, the bam file containing common reads contain alignment information based on reference genome used for bam file used under -j option.

Command Example

java -jar PAINT.jar FindCommonSpecificReads -i "bam_file_from_species1.bam" -o "bam_file_from_species2.bam" -o outputDirectory