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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SYSTEM REQUIREMENTS

AGELESS Package  

Example Data

Divide a Merged Allele File

This page walks you though various steps required to generate Individual Chromosome Files from merged Allele file

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
3) Generate an allele file using findAlleles utility of PAINT
4) Generate an list file using listAlleles utility of PAINT
5) Find parental SNVs using findSNPsSomy utility of PAINT. Extract Homozygous SNVs from the parental lines and place them in a directory.
6) Generate a merged allele file using findAllelesSNPpositions utility of PAINT.

How to Run it?

Divide the merged allele file into individual chromosome files using the DivideMergedFiles2ChrFiles utility of PAINT. Type java -jar PAINT.jar DivideMergedFiles2ChrFiles -h for options.
  • -i is the merged allele file generated using findAllelesSNPpositions utility of PAINT
  • -j is "AlleleFile" because input -i to the program is a merged allele file
  • -o is the directory where individual allele files are written

Command Example

java -jar PAINT.jar DivideMergedFiles2ChrFiles -i "../DemoData/otherFiles/mergedAlleles.txt" -o "../DemoData/individualMergedAlleleFiles" -j "AlleleFile"

Output

The output of the DivideMergedFiles2ChrFiles program looks as follows:
Divide merged allele
As shown in the figure, the merged allele is split into individual chromsome files. Each file contains information corresponding to a chromosome. The partial contents of chromosome 1 file are also shown.
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