Bora Uyar, Dilmurat Yusuf (RBC)
17-18 August 2016
MDC - Berlin
In this course we aim to give the attendees an understanding and hands-on experience of how to do file handling, input/output operations, chaining different tools to each other and being able to re-use workflows in Galaxy. We will use RNA-Seq differential expression analysis as a model to demonstrate the capabilities of Galaxy.
In this tutorial we will introduce:
1. Basics of Galaxy: pages, histories, data libraries, workflows, libraries
2. Types of files typically used in RNA-seq analysis
3. QC (quality control) of the raw sequence data
4. Trimming the reads for quality and for adaptor sequences
5. Aligning RNA-seq reads
6. Quantifying the expression level of genes from read alignments
7. Finding differentially expressed genes
8. Building new workflows and modifying existing workflows
The target audience of this course is wet-lab biologists with limited bioinformatics skills, however you are welcome to attend if you are a bioinformatician who wants to find out about how Galaxy works.
Galaxy, RNA-seq, reproducible workflows
Galaxy platform, FastqGroomer, FastQC, TrimGalore, Tophat, htseq-count, Deseq2