We will investigate the following items:

Quality control of the sequence reads to detect biases or contaminating adapters
Mapping of the reads to the reference genome with use of a transcript database model
Quality control of the mapping results
Adjusting the mapping data to compensate for artefacts like duplicates
Calculate transcript counts usable for differential expression and merging of count tables
Computing differential expression using EdgeR and DESeq2

The code pieces used during the training are made available through our Wiki as well as detailed results and can be copied and adapted for own user needs with minimal edits. Key results have been saved to our server and can be downloaded to fully reproduce the training.