Welcome to this introductory course about NGS data analysis and visualization. During this course you will learn the basics of NGS data analysis and visualization in a Linux environment, current used software and best practices will be explained. This course is focused in NGS data alignment for both DNA and RNA (RNA-seq), variant calling, differential expression analysis and data visualization.
This is course is scheduled for a 3 days and assumes a very basic knowledge of NGS data analysis and Linux. All materials in this is course are free and open, feel free to reuse them as you want. All the data for the tutorials are available in our DropBox folder.
During this first day we will start with an introduction to NGS technology and in the data preparation for their analysis. You will also learn the basics of the GNU/Linux shell introduction. At this point we are ready to start preparing and working with the data: Quality Control (QC) and NGS data alignment.
- Presentation [PDF | OpenOffice]
Very brief overview about NGS technologies and some concepts.
- Presentation [PDF | OpenOffice]
- Presentation - Tutorial - Data
- Presentation [PDF | OpenOffice] - Tutorial
During the second day we will focus on Variant Calling and Data Visualization of DNA and RNA-seq alignments together with VCF files.
- Presentation || Guided example || Tutorial 1 || Tutorial 2
- Presentation || Tutorial 1 || Tutorial 2 || Tutorial 3
- Presentation || Annovar || HPG-Variant
- Presentation || Data
In the last day we will work on RNA-seq data analysis
- Presentation - Tutorial - Data
This course is usually carried out by experienced researchers from CIPF, EMBL-EBI and University of Cambridge. You can ask any question to David Montaner (dmontaner@cipf.es), Marta Bleda (mb2033@cam.ac.uk) and Ignacio Medina (imedina@ebi.ac.uk).