Chapter 11
Analysis of Assemblies and Alignments

  11.1 Finding polymorphisms
   11.1.1 Find Variations/SNPs
  11.2 Analyzing Expression Levels
   11.2.1 Calculating Expression Levels
   11.2.2 Comparing Expression Levels
   11.2.3 Geneious Method for Comparing Expression Levels
   11.2.4 DESeq2 Method for Comparing Expression Levels
   11.2.5 Results
   11.2.6 Principal Component Analysis for DESeq2 results
   11.2.7 Volcano Plots
   11.2.8 Comparing Expression Levels Using the DESeq2 Method on Linux Systems