 |  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 Bottle Brush PlotsThis page walks you though various steps required to generate bottle brush plots using PAINT package.Pipeline1) 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 files using findAlleles utility of PAINT 4) Generate an list files 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 merged allele file using findAllelesSNPpositions utility of PAINT 7) Generate merged allele frequency file using findAlleleFreqsSNPpositions utility of PAINT 8) Divide the merged allele file into individual files using DivideMergedFiles2ChrFiles utility of PAINT. 9) Divide the merged allele frequency file into individual files using DivideMergedFiles2ChrFiles utility of PAINT. 10) Find parental allele frequencies using getParentAllelFrequencies utility of PAINT. 11) Find coverage using findReadDepth utility of PAINT 12) Divide the coverage files into individual chromosome coverage files using divideReadDepthFile utility of PAINT 13) Update all file locations and other information where it says " #UPDATE" in the script../DemoData/Scripts/DrawParFreqPloidyEachLocii.R 14) Use the script ../DemoData/Scripts/DrawParFreqPloidyEachLocii.R to generate the bottle brush plots. Sample Output
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