This course offers an introduction to RNASeq analyses using two different workflow management systems: Galaxy and TOGGLe. This includes reference-based mapping, estimates of transcript levels, differential expression (DE) analyses, visualization of statistics results. Prerequisites Workflow management system (Galaxy, TOGGLe)
Program Mapping of RNASeq against a transcriptome reference with kallisto (Galaxy) Mapping of RNASeq against an annotated genome reference with TopHat (TOGGLe) Differential expression analysis using EdgeR and DESeq2 Plots, clustering, co-expression network: degust, WGCNA
Learning objectives Manipulate packages/tools available for searching DE genes Think about different normalisation methods Detect differentially expressed genes Compare results between two approaches