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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Example Data

Divide Coverage Files

This page walks you though various steps required to generate Individual coverage Files from read depth 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 coverage files using findReadDepth utility of PAINT. Place all the coverage files in one directory

How to Run it?

Divide each coverage file into individual chromosome coverage files using the divideReadDepthFile utility of PAINT. Type java -jar PAINT.jar divideReadDepthFile -h for options.
  • -i is the coverage file generated using divideReadDepthFile utility of PAINT
  • -o is the directory where individual depth files are written

Command Example

java -jar PAINT.jar divideReadDepthFile -i "..\DemoData\readDepth\LV39c5Hyg_srt.depth" -o "..DemoData\individualDepthFiles\LV39c5Hyg_srt"

Output

The output of the divideReadDepthFile ulitity  looks as follows:
individual coverage files
As shown in the figure, the coverage file is split into individual coverage files. Each file contains information corresponding to a chromosome. The partial contents of chromosome 6 file are also shown.
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