Welcome to this introductory NGS data analysis course. During this course you will learn the basics of NGS data analysis in a Linux environment using most currently 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. Data for the tutorials are available in our DropBox folder.
During this first day we will focus in a NGS data introduction and preparing the data for their analysis. The course starts with a short presentation and a NGS data and GNU/Linux shell introduction. Then we will start working and preparing 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 - Tutorial - Data
This course is usually carried out by experienced researchers from CIPF and EMBL-EBI. You can ask any question to David Montaner ([email protected]), Marta Bleda ([email protected]) and Ignacio Medina ([email protected]).