RNA-Seq analysis for differential expression in GenePattern

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.

Target audience: Life Science Researchers, PhD students, beginner bioinformaticians, post-docs

Authors: Janick Mathys and Guy Bottu

Remote created date: 2016-04-22

Remote updated date: 2017-10-09

RNA-Seq analysis for differential expression in GenePattern https://tess.elixir-europe.org/materials/rna-seq-analysis-for-differential-expression-in-genepattern 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. Life Science Researchers PhD students beginner bioinformaticians post-docs 2016-04-22 2017-10-09