Difference between revisions of "INF-BIOX121 H14 course material"
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== File formats == | == File formats == | ||
− | [ | + | [[Media:HTS 2014 Day01 File formats.pdf|File formats presentation]] |
− | [ | + | [[Media:HTS 2014 Day01 File formats-exercises.pdf|File formats exercises]] |
== Quality control == | == Quality control == | ||
− | [ | + | [[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/ | + | Some more information on 'duplication levels': [https://www.biostars.org/p/107402/ https://www.biostars.org/p/107402/] |
== miRNA == | == miRNA == | ||
− | [ | + | [[Media:HTS 2014 microRNA theory IB 14.pdf|microRNA theory]] |
− | [ | + | [[Media:HTS 2014 Intro Galaxy Lifeportal.pdf|Intro Galaxy Lifeportal]] |
− | [ | + | [[Media:HTS 2014 miRNA analysis Lifeportal 14 final.pdf|miRNA analysis Lifeportal]] |
+ | |||
+ | [[Media:EdgeR.pdf|EdgeR]] | ||
+ | |||
+ | [[Media:HTS 2014 microRNA analysis INFBIO 14.pdf|microRNA analysis]] | ||
+ | |||
+ | [[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]. | ||
+ | |||
+ | 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 == | ||
+ | |||
+ | Lex Nederbragt: [[Media:141014 Thoughts on reproducibility INF BIOx121.pptx.pdf|Thoughts on reproducibility]] | ||
+ | |||
+ | Karin Lagesen: [[Media:Dataressurser.pdf|Working with data]] | ||
+ | |||
+ | Jon Lærdahl: [[Media:BioinformaticsCoreFacilityOutreach-E1.pdf|Oslo Bioinformatics Core Facility & Elixir Noway]] | ||
+ | |||
+ | Jon Lærdahl: [[Media:DatabasesOnTheWeb-A1.pdf|Bioinformatics resources on the web]] | ||
+ | |||
+ | Martin Malmstrøm: [[Media:HTS_2014_Martin_Malsmtroem.pdf|If I can, YOU can! - From seal cuddling to hardcore bioinformatics]] | ||
+ | |||
+ | Rolf Skotheim: [[Media:HTS 2014 Rolf Skotheim.pdf|Selected bioinformatics approaches to identify RNA changes in cancer]] | ||
== RNAseq == | == RNAseq == | ||
+ | |||
+ | [[Media: HTS 2014 RNAseq introduction.pdf|RNAseq introduction]] | ||
+ | |||
+ | [[Media: HTS 2014 RNAseq applications.pdf|RNAseq applications]] | ||
+ | |||
+ | == ChIP-seq == | ||
+ | |||
+ | [[Media:HTS 2014 ChIPSeq module.pdf|ChIP-seq slides]] | ||
+ | |||
+ | [[Media:HTS 2014 chip-seq-practical.pdf|ChIP-seq practical]] | ||
== Variant calling == | == Variant calling == | ||
− | + | [[Media:HTS 2014 variantCallingCourse sept2014 Part1.pdf|Variant Calling Part 1]] | |
+ | |||
+ | [[Media:HTS_2014_variantCallingCourse_sept2014_Part2.pdf|Variant Calling Part 2]] | ||
== Statistical genomics == | == Statistical genomics == | ||
+ | |||
+ | [[Media:HTS_2014_Statistical_genomics_part_1.pdf|Statistical genomics part 1]] | ||
+ | |||
+ | [[Media:HTS_2014_Statistical_genomics_part_2.pdf|Statistical genomics part 2]] | ||
+ | |||
+ | [[Media:HTS_2014_Data_upload_and_track_types.pdf|Data upload and track types]] | ||
+ | |||
+ | [[Media:HTS_2014_Elixir.no_and_NeLS.pdf|Elixir.no and NeLS]] | ||
+ | |||
+ | [[Media:HTS 2014 MS data.txt|MS data]] |
Latest revision as of 12:43, 29 October 2014
Contents
Introduction
HTS_2014_SequencingTech&Applic_Meza-Zepeda.pdf
File formats
Quality control
Fastqc manual: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
Some more information on 'duplication levels': https://www.biostars.org/p/107402/
miRNA
De novo assembly
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