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