Bulk RNASeq in Galaxy: from reads to counts
General context
This course has changed date from 3rd to the 6th of March! The training will be held in the Park Inn Hotel in Leuven.
Galaxy software framework is an open-source application. It is a system that enables researchers without informatics expertise to perform computational biology analyses through the web.
This practical aims to familiarize you with the Galaxy user interface & execute a complete analysis of RNA-seq data.
It will teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows, and sharing your work. In this tutorial we will introduce you to bare basics of Galaxy:
- Getting data from external databases such as UCSC
- Performing simple data manipulation
- Understanding Galaxy’s History system
- Creating and running a workflow
The RNA-seq data analysis part comprises:
- Filtering and quality control of reads
- Mapping of reads to reference genomes
- Read summarization and read count modes
This workshop is organised by ELIXIR Belgium. The course will handle the data analysis of bulk RNA-seq up till counts data. The subsequent part of the data analysis (differential expression) will be addressed during the course "Bulk RNASeq: from counts to differential expression".
Biologists and other life science researchers who would like an introduction to Galaxy, its workflows and use it for NGS analysis.
Familiarity with the Illumina sequencing process and with basic NGS data formats: FASTQ, SAM/BAM, GTF, ...If you do not meet these requirements you have to follow the "Introduction to the analysis of NGS data" training first.
Trainers
Janick Mathys
Janick tries to help VIB scientists analyze their data by offering bioinformatics training and support. Next to organizing trainings, creating e-learning courses and teaching statistics, R, Python, Linux, HPC, bulk and single cell RNA-Seq analysis, she consults scientists and develops pipelines for omics analyses. Before joining VIB, she worked as a post-doc at KULeuven, doing research on transcriptomics and transcription regulation. She coordinated the Master of Bioinformatics program of KULeuven and taught the course on Biological Databases.
Program
Working with Galaxy user interface
RNA-seq analysis with Galaxy
Practical info
06 March 2020
Leuven - Park Inn by Radisson
Martelarenlaan 36
3010 Leuven
Belgium
06 March 2020
Leuven - Park Inn by Radisson
The hotel is located 300m from Leuven Central Station, just a short 5 minute walk.
06 March 2020
Leuven - Park Inn by Radisson
Using your bike for longer distances? Check Cycle Highways.
06 March 2020
Leuven - Park Inn by Radisson
Underground P1-Parking Station Leuven, Martelarenlaan 4, 3010 Leuven or parking De Bond, Martelarenlaan 18, 3010 Leuven.
06 March 2020
Leuven - Park Inn by Radisson
+32 16 61 66 02
sales.leuven@parkinn.com