Welcome and introduction

Agenda, resources and other useful information

Welcome!

Welcome to this bioinformatics course on RNA-Seq and Somatic-Seq.During this course you will learn the basics of RNA-seq data analysis in a Linux environment, current used software and best practices will be explained. This is course is scheduled for a 2 days and assumes a very basic knowledge of NGS data analysis and Linux. All materials in this is course are free and open and derived from some public avaible online course.

Data for tutorial

ALL DATA

rna_salmon tutorial

rna_kallisto_sleuth

rna_fusion

[Somatic_call] (https://drive.google.com/file/d/1DqFQ86BDmfjNjjQ5hoA0ddXlp8z-UPZ4/view?usp=sharing)

Here you can found and Interesting video that explain NGS sequencing

Learning outcomes

After this course you should be able to:

• Understand the problems on RNA-seq data analisys
• Know the precincipal formats and workflow for RNA-Seq and Somatic-Seq
• Evaluate the results of RNA-Seq
• Plan experiments oon RNA-seq
• Detect Fusion genes

and you will be exposed to these software:

• FASTC
• SAMTOOLS
• bedtools
• bwa
• bowtie2
• multiQC
• STAR
• vt
• freebays
• GATK
• NEXTFLOW
• KALLISTO
• SLEUTH
• picards
• Salmon
• Shiny

NGS data can be big, very big, huge! Biology is now a Big Data science There are not many web-based or graphical applications to perform analysis yet, sorry. Most tools developed to work on Linux, many command line programs How to work in NGS?

• Small datasets (<1TB): workstations
• Medium sized datasets (<100TB): clusters
• Big datasets (100TB-20PB): big clusters and/or cloud based solutions

Exercises during this course the NGS alignment will be done using the human chromosome 22. By doing this we can speed up exercises and avoid using too much memory. Under real circumstances, when using the standard reference genome, all the commands are exactly the same. Some software has been already installed. During the practicl we install the other. However, it’s usually good to learn the basics of software installation in Linux, there is an optional session at the end of the first day for those that want to learn how to install NGS software in a standard Linux. We use conda for install most of the tools.

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We assume you are familiar with:

• Next generation sequencing in general
• Be patient
• Please see this video How to sequence the human genome - Mark J. Kiel
• R base manipulation

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Agenda

22 march 2018

Title	Lecture/Practical
Introduction & overview of RNA-seq	Lecture
Differential expression analisys	Lecture / Practical
Fusion identitification	Lecture / Practical[optional]

23 march 2018

Title	Lecture/Practical
Somatic calling	Lecture /Practical
GATK best practize	Lecture /Practical