Difference between revisions of "INF-BIOX121 H14 course material"

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== Statistical genomics ==
 
== Statistical genomics ==
  
[[Media:HTS_2014_MS_data.txt|MS data]]
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[[Media:HTS 2014 Statistical genomics part 1.pdf|Statistical genomics part 1]]
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 +
[[Media:HTS 2014 Statistical genomics part 2.pdf|Statistical genomics part 2]]
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[[Media:HTS 2014 Data upload and track types.pdf|Data upload and track types]]
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[[Media:HTS 2014 Elixir.no and NeLS.pdf|Elixir.no and NeLS]]
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 +
[[Media:HTS 2014 MS data.txt|MS data]]

Revision as of 11:41, 29 October 2014

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

Martin Malmstrøm: If I can, YOU can! - From seal cuddling to hardcore bioinformatics

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

RNAseq

RNAseq introduction

RNAseq applications

ChIP-seq

ChIP-seq slides

ChIP-seq practical

Variant calling

Variant Calling Part 1

Variant Calling Part 2

Statistical genomics

Statistical genomics part 1

Statistical genomics part 2

Data upload and track types

Elixir.no and NeLS

MS data