Educators:
Bora Uyar, Dilmurat Yusuf (RBC)
Date:
17-18 August 2016
Location:
MDC - Berlin
Contents:
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.
Learning goals:
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
Prerequisites:
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.
Keywords:
Galaxy, RNA-seq, reproducible workflows
Tools:
Galaxy platform, FastqGroomer, FastQC, TrimGalore, Tophat, htseq-count, Deseq2
Contact:
Bora Uyar
Dilmurat Yusuf