 |  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 line PlotsThis page walks you though various steps required to generate line 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) Update the script ../DemoData/Scripts/LinePlots.R where it says "#UPDATE" and use the script to generate the bottle brush plots. Sample Output
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