AGELESSMolecularMicro

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

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




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Find Reads aligned to both the genomes and to respective genomes maintaining synteny

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 that are syntenic and the 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 FindCommonSpecificReadsChrWise utility of PAINT package takes sorted bam file and finds reads common to both the genomes maintaining synteny and those specific to individual genomes respectively. Type java -jar PAINT.jar FindCommonSpecificReadsChrWise -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 maintaining synteny. 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.
  • -k is the file containing information regarding synteny. This file contains two columns first column contains chromosome names from species 1 and the second column contains chromosome names from species 2 that are in synteny with chromosome names in column 1. Both the columns are separated by tab.

Command Example

java -jar PAINT.jar FindCommonSpecificReadsChrWise -i "bam_file_from_species1.bam" -o "bam_file_from_species2.bam" -o outputDirectory -k ChromosomesWithSynteny