 |  PAINT: Leishmania Sexual Reproductive Strategies As Resolved Through Compuational Methods Designed for Aneuploid Genomes |  |
MAIN INDEX ANALYTICAL PIPELINE CONTACT SYSTEM REQUIREMENTS PAINT Package Example Data | Generate Heatmap of ploidiesThis page walks you though various steps required to generate a heatmap of ploidies using PAINT package.Prerequisites1) 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 read depth (coverage) for each of the samples using findReadDepth utility of PAINT 4) Generate concatenated ploidy matrix using ConcatenatedPloidyMatrix utility of PAINT How to Run it?The R script to generate the heat map is in the directory ../DemoData/scripts/heatmap.R . The location of the concatenated ploidy matrix needs to be updated in the R script. It is marked using "#UPDATE" in the script. Also, it requires "gplots" package in R to draw the heatmap.OutputThe output of the listAlleles program looks as follows:
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