Difference between revisions of "INF-BIOX120 H13 course material"

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== Introduction  ==
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[[Media:SequencingTech%26Applic_INF-BIO_2013.pdf|Introduction to High-throughput sequencing technologies and applications]] (pdf)<br>
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== File formats  ==
 
== File formats  ==
  
 
[[Media:HTS_Course_file_formats.pdf|HTS_Course_file_formats]] (pdf)<br>[[Media:HTS_Course_file_formats_exercises.pdf|HTS_Course_file_formats_exercises]] (pdf)<br>  
 
[[Media:HTS_Course_file_formats.pdf|HTS_Course_file_formats]] (pdf)<br>[[Media:HTS_Course_file_formats_exercises.pdf|HTS_Course_file_formats_exercises]] (pdf)<br>  
  
== Quality control ==
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== Quality control ==
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[https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly/blob/master/practicals/00_Read_QC.md Read QC practical]&nbsp;(webpage)
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== miRNA  ==
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[https://wiki.uio.no/projects/clsi/images/0/0f/MicroRNA_theory.pdf microRNA_theory] (pdf)<br> [https://wiki.uio.no/projects/clsi/images/f/fb/MicroRNA_analysis.pdf microRNA_analysis] (pdf)<br> [http://www.biomedcentral.com/1471-2164/13/320 Baboon_miRNA] (link to article)<br> [https://wiki.uio.no/projects/clsi/images/7/74/EdgeR.pdf edgeR] (pdf)<br> [https://wiki.uio.no/projects/clsi/images/9/99/MiRNA_analysis_infbio_practicals.pdf miRNA_analysis_infbio_practicals] (pdf)
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== RNAseq  ==
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[https://wiki.uio.no/projects/clsi/images/d/da/RNAseq_introduction180913.pdf RNAseq_introduction180913]&nbsp;(pdf)<br>[https://wiki.uio.no/projects/clsi/images/2/26/Introduction_Differential_Expression.pdf Introduction Differential Expression] (pdf)<br>[https://wiki.uio.no/projects/clsi/images/4/42/INF-BIOx120_RNASeq_Analysis.pdf INF-BIOx120 RNASeq Analysis] (pdf)<br>[https://wiki.uio.no/projects/clsi/images/e/e0/Commands.txt commands.txt]
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== Variant calling  ==
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[https://wiki.uio.no/projects/clsi/images/8/80/VariantCallingCourse_sept2013_Part1.pdf variantCallingCourse_sept2013_Part1](pdf)&nbsp;
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[https://wiki.uio.no/projects/clsi/images/3/3d/VariantCallingCourse_sept2013_Part2.pdf variantCallingCourse_sept2013_Part2] (pdf)
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== ''De novo'' assembly  ==
  
[https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly/blob/master/practicals/Read_QC.pdf?raw=true Read QC] (pdf)
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See this github repo:&nbsp;[https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly]
  
== miRNA ==
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== Statistical genomics ==
  
microRNA_analysis (pdf)<br>microRNA_theory (pdf)<br>Baboon_miRNA (pdf)<br>edgeR (pdf)<br>miRNA_analysis_infbio_practicals (pdf)<br>
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[https://wiki.uio.no/projects/clsi/images/b/b6/StatisticalGenomics_part_1.pdf StatisticalGenomics_part_1] (pdf)<br>[https://wiki.uio.no/projects/clsi/images/8/87/StatisticalGenomics_part_3.pdf StatisticalGenomics_part_3] (pdf)<br>[https://wiki.uio.no/projects/clsi/images/4/41/StatisticalGenomics_part_4.pdf StatisticalGenomics_part_4] (pdf)<br>[https://wiki.uio.no/projects/clsi/images/3/31/Pres_ChoiceOfWaysOfInteractingWithBioinformatics_v2.pdf ChoiceOfWaysOfInteractingWithBioinformatics] (pdf)<br>

Latest revision as of 12:51, 7 October 2013

Introduction

Introduction to High-throughput sequencing technologies and applications (pdf)

File formats

HTS_Course_file_formats (pdf)
HTS_Course_file_formats_exercises (pdf)

Quality control

Read QC practical (webpage)

miRNA

microRNA_theory (pdf)
microRNA_analysis (pdf)
Baboon_miRNA (link to article)
edgeR (pdf)
miRNA_analysis_infbio_practicals (pdf)

RNAseq

RNAseq_introduction180913 (pdf)
Introduction Differential Expression (pdf)
INF-BIOx120 RNASeq Analysis (pdf)
commands.txt

Variant calling

variantCallingCourse_sept2013_Part1(pdf) 

variantCallingCourse_sept2013_Part2 (pdf)

De novo assembly

See this github repo: https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly

Statistical genomics

StatisticalGenomics_part_1 (pdf)
StatisticalGenomics_part_3 (pdf)
StatisticalGenomics_part_4 (pdf)
ChoiceOfWaysOfInteractingWithBioinformatics (pdf)