Preface

The high throughput RNA-sequencing technology has been widely used and has advanced our understanding of RNA biology. The process of RNA-sequencing can be divided in two parts; 1) Generating the data from biological sample and 2) Computational data analysis. This book is about the second part which is usually done with a subset of many related software, refered as pipeline. For ease of biologist, there are many predefined and I have been analyzing RNA-seq data from 2014 using different. This book is an attempt to describe how to use the pipeline 4-RNA-seq and it is also a collection of the study materials which has been used in RNA-seq section of the course Advanced course in genomics and gene regulation 2019 by me.

Structure of the book

Chapter 1 and 2 explains the step wchich are executed from a unix terminal. Chapter 3 describes the final data analysis step which requires R and can be performed in any OS. Chapter 4 explains 4-RNA-seq pipleline which to execute chapter 1 and 2 commands in easier and efficient ways. Therefore chapter 1 to 3 is must for beginner and chapter 4 is for who have slurm environment and looking for a pipeline to execute RNA-seq data.

Chapter 1: Quality Control

Description of quality assessment, filtering ribosomal RNA and bad reads of fastq files with fastqc, multiqc, sortmerna and trimmomatic.

Chapter 2: Alignment and count

Alighnment of reads and count values from fastq and bam files using toll like star and htseq-count.

Chapter 3: Read count analysis

Differential expression analysis with R package DESeq2.

Chapter 4: Pipeline:4-RNA-seq

A step by step instruction for 4-RNA-seq pipeline execution.

Acknowledgement

Most of the study material are motivated from Rna-seq data analysis, Workshop II 1-3.11.2016. This could not be possible without the encouragement and permission from the istructor/author of the workshop. I like to thank
* Nicolas DelHomme, Umeå University, Sweden
* Bastian Schiffthaler, Umeå University, Sweden
* Charlotte Soneson, Friedrich Miescher Institute for Biomedical Research
* Petri Törönen, University of Helsinki for reviewing this book.

The online version of this book is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.