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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
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