Monday – Classes from 2-8 pm Berlin time
* Session 1- Intro to the RNA-Seq de novo assembly workshop
* Intro to RNA-Seq, Next-gen sequence analysis and the workshop setup
* Practical: exploring the computational infrastructure
* Session 2- Read quality assessment and trimming
* Practical: using FASTQC, TRIMMOMATIC, MultiQC
* Session 3- Short Read de novo assembly
* Overview of de novo transcriptome assembly
* Practical: assemble rna-seq data using ORP
Tuesday – Classes from 2-8 pm Berlin time
* Session 4- Long read sequencing
* Practical- Starting the PacBio preprocessing
* Overview of long read sequencing for RNA-Seq
* Practical- PacBio IsoSeq preprocessing
Wednesday – Classes from 2-8 pm Berlin time
* Session 5- Assembly comparisons
* Initial data exploration: assembly quality, and QC samples and replicates
* Practical: visualization using IGV / JBrowse
* Practical: Bioloqical Quality Assessment (PCA, etc.)
* Session 6- Intro to expression quantification using RNA-Seq and Differential expression analysis
* Overview of statistical methods for differential expression (DE).
* Practical: quantify expression and using Bioconductor tools for DE analysis
Thursday – Classes from 2-8 pm Berlin time
* Session 7- Functional annotation and Functional enrichment studies
* Overview of methods for functional annotation
* Practical: applying Trinotate to find coding regions in transcripts and predict biological function.
* Session 9- Overview of functional enrichment analysis
* Practical: applying GOseq to identify significantly enriched Gene Ontology categories among transcript clusters.
Friday – Classes from 2-8 pm Berlin time
* Session 10- Review and custom data analyses