The Power of RNA-seq

Wageningen, June 11-13 2018

Program

Evaluation form

Day 1

Hand outs

• 1a Introduction
• 1a NGS
• 1b RNAseq
• 1c Assembly, annotation, quantification

Practicals

• 1b Mapping
• 1c Quantification

Data files

• ST_1.fastq
• SRR5304927_1.fastq
• SRR5304927.zip
• ST_vs_HT.csv

Day 2

Hand outs

• 2a Differential Expression
• 2b Clustering

Practicals

• 2a Differential Expression
• 2b Clustering (answers)

Data files

• kallisto.zip
• km.txt
• hc.txt
• wgcna_edges.txt
• wgcna_nodes.txt

Day 3

Hand outs

• 3a Interpretation
• Tulip and Lily transcriptomes

Practicals

• 3a Interpretation

Links

• Linux command-line tutorial (interactive)
• Sleuth walkthroughs
• Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
• Analyzing RNA-seq data with DESeq2
• De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis