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