Monday 12th – Classes from 09:30 to 17:30
Session 1- Intro to the Trinity RNA-Seq workshop
Intro to RNA-Seq
Intro to next-gen sequence analysis
Overview of unix and workshop setup
o Practical: exploring the computational infrastructure
Read quality assessment and trimming
o Practical: using FASTQC and TRIMMOMATIC
Tuesday 13th – Classes from 09:30 to 17:30
Session 2-Trinity de novo assembly, expression quantitation, and assembly QC
Overview of Trinity de novo transcriptome assembly
o Practical: assemble rna-seq data using Trinity
Intro to expression quantification using RNA-Seq
o Practical: quantify expression for Trinity assembly
Initial data exploration: assembly quality, and QC samples and replicates
o Practical: using IGV
o Practical: replicate correlation matrix and PCA
Wednesday 14th – Classes from 09:30 to 17:30
Session 3- Differential expression analysis
Overview of statistical methods for differential expression (DE).
o Practical: using Bioconductor tools for DE analysis.
Transcript clustering and expression profiling
o Practical: generating heatmaps and extracting transcript clusters.
Thursday 15th – Classes from 09:30 to 17:30
Session 4-Functional annotation and Functional enrichment studies
Overview of methods for functional annotation
o Practical: applying Trinotate to find coding regions in transcripts and predict biological function.
Overview of functional enrichment analysis
o Practical: applying GOseq to identify significantly enriched Gene Ontology categories among transcript clusters.
Friday 16th – Classes from 09:30 to 17:30
Session 5- Review and custom data analyses
