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

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== File formats ==
 
== File formats ==
  
[https://wiki.uio.no/projects/clsi/images/5/5c/HTS_2014_Day01_File_formats.pdf HTS_2014_Day01_File_formats.pdf]
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[[Media:HTS 2014 Day01 File formats.pdf|File formats presentation]]
  
[https://wiki.uio.no/projects/clsi/images/3/37/HTS_2014_Day01_File_formats-exercises.pdf HTS_2014_Day01_File_formats-exercises.pdf]
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[[Media:HTS 2014 Day01 File formats-exercises.pdf|File formats exercises]]
  
 
== Quality control ==
 
== Quality control ==
  
[https://wiki.uio.no/projects/clsi/images/d/de/HTS_2014_read_qc.pdf HTS_2014_read_qc.pdf]
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[[Media:HTS 2014 read qc.pdf|Read QC practical]]
  
 
Fastqc manual: [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/]
 
Fastqc manual: [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/]
  
Some more information on 'duplication levels': [https://www.biostars.org/p/107402/ [1]]
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Some more information on 'duplication levels': [https://www.biostars.org/p/107402/ https://www.biostars.org/p/107402/]
  
 
== miRNA ==
 
== miRNA ==
  
[https://wiki.uio.no/projects/clsi/images/b/be/HTS_2014_microRNA_theory_IB_14.pdf HTS_2014__microRNA_theory_IB_14.pdf]
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[[Media:HTS 2014 microRNA theory IB 14.pdf|microRNA theory]]
  
[https://wiki.uio.no/projects/clsi/images/3/32/HTS_2014_Intro_Galaxy_Lifeportal.pdf HTS_2014_Intro_Galaxy_Lifeportal.pdf]
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[[Media:HTS 2014 Intro Galaxy Lifeportal.pdf|Intro Galaxy Lifeportal]]
  
[https://wiki.uio.no/projects/clsi/images/2/2f/HTS_2014_miRNA_analysis_Lifeportal_14_final.pdf HTS_2014_miRNA_analysis_Lifeportal_14_final.pdf]
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[[Media:HTS 2014 miRNA analysis Lifeportal 14 final.pdf|miRNA analysis Lifeportal]]
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[[Media:EdgeR.pdf|EdgeR]]
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[[Media:HTS 2014 microRNA analysis INFBIO 14.pdf|microRNA analysis]]
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[[Media:HTS 2014 miRNA analysis CL.pdf|miRNA analysis Command Line]]
  
 
== De novo assembly ==
 
== De novo assembly ==
  
 
See [https://github.com/lexnederbragt/INF-BIOx121_fall2014_de_novo_assembly this github repository].
 
See [https://github.com/lexnederbragt/INF-BIOx121_fall2014_de_novo_assembly this github repository].
 +
 +
Also, have a look at [http://www.slideshare.net/flxlex/assembly-before-and-after this presentation] on different aspects of assembly we didn't manage to go through.
  
 
== How to become an efficient bioinformatician ==
 
== How to become an efficient bioinformatician ==
  
Lex Nederbragt: [https://wiki.uio.no/projects/clsi/images/7/75/141014_Thoughts_on_reproducibility_INF_BIOx121.pptx.pdf Thoughts on reproducibility]
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Lex Nederbragt: [[Media:141014 Thoughts on reproducibility INF BIOx121.pptx.pdf|Thoughts on reproducibility]]
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Karin Lagesen: [[Media:Dataressurser.pdf|Working with data]]
  
 
Jon Lærdahl: [[Media:BioinformaticsCoreFacilityOutreach-E1.pdf|Oslo Bioinformatics Core Facility & Elixir Noway]]
 
Jon Lærdahl: [[Media:BioinformaticsCoreFacilityOutreach-E1.pdf|Oslo Bioinformatics Core Facility & Elixir Noway]]
  
Jon Lærdahl: Bioinformatics resources on the web
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Jon Lærdahl: [[Media:DatabasesOnTheWeb-A1.pdf|Bioinformatics resources on the web]]
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Martin Malmstrøm: [[Media:HTS_2014_Martin_Malsmtroem.pdf|If I can, YOU can! - From seal cuddling to hardcore bioinformatics]]
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Rolf Skotheim: [[Media:HTS 2014 Rolf Skotheim.pdf|Selected bioinformatics approaches to identify RNA changes in cancer]]
  
 
== RNAseq ==
 
== RNAseq ==
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[[Media: HTS 2014 RNAseq introduction.pdf|RNAseq introduction]]
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[[Media: HTS 2014 RNAseq applications.pdf|RNAseq applications]]
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== ChIP-seq ==
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[[Media:HTS 2014 ChIPSeq module.pdf|ChIP-seq slides]]
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[[Media:HTS 2014 chip-seq-practical.pdf|ChIP-seq practical]]
  
 
== Variant calling ==
 
== Variant calling ==
  
== ChIP-seq ==
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[[Media:HTS 2014 variantCallingCourse sept2014 Part1.pdf|Variant Calling Part 1]]
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[[Media:HTS_2014_variantCallingCourse_sept2014_Part2.pdf|Variant Calling Part 2]]
  
 
== Statistical genomics ==
 
== Statistical genomics ==
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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]]

Latest revision as of 11:43, 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