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{"name":"NGS course","tagline":"An introductory course about NGS data analysis","body":"# Overview\r\n\r\nWelcome 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.\r\n\r\nThis 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](https://www.dropbox.com/sh/4qkqch7gyt888h7/AABD_i9ShwryfAqGeJ0yqqF3a).\r\n\r\n\r\n# Schedule\r\n\r\n## Day 1\r\n\r\nDuring 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_.\r\n\r\n### Presentation\r\n- Presentation [[PDF](Course_Materials/presentation/presentation_mda14.pdf) | [OpenOffice](Course_Materials/presentation/presentation_mda14.odp)]\r\n\r\n### Introduction to NGS technologies\r\nVery brief overview about NGS technologies and some concepts.\r\n- [Presentation](Course_Materials/intro-ngs/ngs_introduction_mda14.pdf)\r\n\r\n### Introduction to GNU/Linux shell\r\n- Presentation [[PDF](Course_Materials/intro-linux/intro_Linux_mda14.pdf) | [OpenOffice](Course_Materials/intro-linux/intro_Linux_mda14.odp)]\r\n\r\n### Quality control for NGS raw data (FASTQ)\r\n- [Presentation](Course_Materials/quality_control/presentation/quality_control_presentation.pdf) - [Tutorial](Course_Materials/quality_control/tutorial/quality_control.html) - [Data](https://www.dropbox.com/sh/4qkqch7gyt888h7/AAAqebBSC6JgDGq4emwNORCaa/quality_control)\r\n\r\n\r\n### DNA and RNA-seq read alignment\r\n- Presentation [[PDF](Course_Materials/alignment/presentation/ngs-read-mapping-imedina-mda14.pdf) | [OpenOffice](Course_Materials/alignment/presentation/ngs-read-mapping-imedina-mda14.odp)] - [Tutorial](Course_Materials/alignment/tutorial/example.html)\r\n\r\n\r\n## Day 2\r\n\r\nDuring the second day we will focus on _Variant Calling_ and _Data Visualization_ of DNA and RNA-seq alignments together with VCF files. \r\n\r\n###  NGS data Visualization\r\n\r\n- [Presentation](Course_Materials/visualization/presentation/2014-Cambridge_visualisation.pdf) || [Guided example](Course_Materials/visualization/tutorial/000_example.html) || [Tutorial 1](Course_Materials/visualization/tutorial/010_example.html) || [Tutorial 2](Course_Materials/visualization/tutorial/020_example.html)\r\n\r\n### Variant calling analysis\r\n\r\n- [Presentation](Course_Materials/variant_calling/presentation/2014-Cambridge_variant_calling.pdf) || [Tutorial 1](Course_Materials/variant_calling/tutorial/010_example.html) || [Tutorial 2](Course_Materials/variant_calling/tutorial/020_example.html) || [Tutorial 3](Course_Materials/variant_calling/tutorial/030_example.html)\r\n\r\n### Variant annotation\r\n\r\n- [Presentation](Course_Materials/variant_annotation/presentation/2014-Cambridge_variant_annotation.pdf) || [Annovar](Course_Materials/variant_annotation/tutorial/annovar.html) || [HPG-Variant](Course_Materials/variant_annotation/tutorial/hpg-variant.html)\r\n\r\n### Variant prioritization\r\n\r\n- [Presentation](Course_Materials/variant_prioritization/presentation/2014-Cambridge_variant_prioritization.pdf)\r\n\r\n\r\n## Day 3\r\n\r\n### Association studies\r\n\r\n- [Presentation](Course_Materials/association_studies/presentation/association_studies_presentation.pdf) - [Tutorial](Course_Materials/association_studies/tutorial/association_studies.html)\r\n\r\n### RNA-Seq data analysis\r\n\r\n- [Presentation](Course_Materials/rna_seq/presentation/rna_seq.pdf) - [Tutorial](Course_Materials/rna_seq/tutorial/rna_seq.html) - [Data](https://www.dropbox.com/sh/4qkqch7gyt888h7/AAB77HfUPkiXBj1MmshjyKtYa/rna_seq)\r\n\r\n### Functional analysis\r\n\r\n- [Presentation](Course_Materials/functional/presentation/babelomics_data_analysis.pdf) - [Tutorial](http://bioinfo.cipf.es/babelomicstutorial/)\r\n\r\n\r\n\r\n----\r\n\r\n# About\r\n\r\nThis course is usually carried out by experienced researchers from CIPF and EMBL-EBI. You can ask any question to David Montaner (dmontaner@cipf.es), Marta Bleda (mbleda@cipf.es) and Ignacio Medina (imedina@ebi.ac.uk).\r\n","google":"","note":"Don't delete this file! It's used internally to help with page regeneration."}