INF-BIOX121 H14 course material

Introduction

HTS_2014_SequencingTech&Applic_Meza-Zepeda.pdf

File formats

File formats presentation

File formats exercises

Quality control

Read QC practical

Fastqc manual: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/

Some more information on 'duplication levels': https://www.biostars.org/p/107402/

miRNA

microRNA theory

Intro Galaxy Lifeportal

miRNA analysis Lifeportal

EdgeR

microRNA analysis

miRNA analysis Command Line

De novo assembly

See this github repository.

Also, have a look at this presentation on different aspects of assembly we didn't manage to go through.

How to become an efficient bioinformatician

Lex Nederbragt: Thoughts on reproducibility

Karin Lagesen: Working with data

Jon Lærdahl: Oslo Bioinformatics Core Facility & Elixir Noway

Jon Lærdahl: Bioinformatics resources on the web

Rolf Skotheim: Selected bioinformatics approaches to identify RNA changes in cancer

RNAseq

RNAseq introduction

RNAseq applications

ChIP-seq

ChIP-seq practical

Variant calling

Variant Calling Part 1

Variant Calling Part 2