Welcome to this course

Agenda, resources and other useful information

Welcome!

Welcome to this introductory course about RNA-seq data analysis. 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. We evaluate also some ways to do RNA-seq analisys using galaxy. This course is focused on transcriptomics (RNA-seq) and his shades (Mirna-seq,Fusion-seq,RIP-seq,Ribo-seq). Particular attention was used for demonstrate differents approach. 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 pulic avaible online course.

DropBox folder

data TUTORIAL RNA data2 rnaseq_star Practical

Here you can found and Interesting video that explain NGS sequincing

Learning outcomes

After this course you should be able to:

• Start to move on linux system
• Know the precincipal formats use on NGS
• Evaluate quality and clean fastq
• Map and visualize some alignment
• Know some base of analisys of RNA-seq

and you will be exposed to these software:

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

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 X or 21 or MT as a reference genome. 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 Software has been already installed to save time, so you are not expected to download and install all the software it is going to be used. 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.

---

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

---

Agenda

20 may 2019

Title	Lecture/Practical
Introduction & overview of NGS (RNA seq strategy)	Lecture
Introduction to Linux and R and command line interface	Lecture / Practical
NGS data format	Lecture / Practical

21 may 2019

Title	Lecture/Practical
Introduction to RNA sequencing quality evaluation	Lecture /Practical
RNASeq Analysis Workflow and planning (Quality Control, Alignment, Gene expression quantification, Differential expression analysis)	Lecture /Practical
Other approach on RNA-seq (Fusion detection, variant calling on RNA-seq, miRNA-seq) (lesson/practical)	Lecture