Contents

• Introduction
• Mapping tiling array probes on genome
  • Extacting probe sequences in fasta format
  • Creating the probe annotation files
  
  
• Pre-processing of raw Affymetrix .CEL files
  • Extracting data from .CEL files
  • Normalizing signal
  • Creating a NucleoMiner .db file
  
  
• Inferring nucleosome occupancy
  • Signal with unpredictable trends
  • Detrended signal
  • Threading the inference process
  • Averaging nucleosome occupancy profiles around genomic features
  
  
• Aligning genome sequences
• Aligning nucleosome occupancy profiles
• Looking for Single Nucleosome EpiPolymorphism
  • Creating the dataset
  • Running the ANOVA
  • Computing the FDR
  • Outputting the results
  
  
• Bibliography