Difference: EducationBioinformaticsII-Seq (1 vs. 17)

Revision 17
16 Oct 2015 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
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R & Bioconductor

  • R tutorials
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Revision 16
12 Oct 2015 - Main.AngelaLuijf
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META TOPICPARENT name="EducationBioLab"
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Bioinformatics-II: Next Generation Sequencing. RNA-Seq and Exome sequencing

During this bioinformatics programme the participants acquire fundamental skills in Next Generation Sequencing (NGS) and the analysis of NGS data. In particular we will focus on 'exome sequencing' and 'RNA-Seq'.
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  • Location: Academic Medical Center, Amsterdam. See here how to get there.
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  • Location: Academic Medical Center, Amsterdam. See here how to get there.
 
  • Course material: All course material is provided during the course.
  • ECTS: 6
  • Coordinator: Antoine van Kampen
Revision 15
29 Sep 2014 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
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Medical Bioinformatics

 
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Revision 14
31 Mar 2014 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  Note: This course focuses on the analysis of NGS data. This part of the programme 'bioinformatics' doesn't consider any aspect of GRID (computing).

Course outline and schedule

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Background information

Next-generation sequencing reviews

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454 and Solid sequencing technology

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Sequencing technology

 

RNA-Seq

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Exome sequencing

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Bias in sequencing data

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Tools and data for computer exercises

Important note: for the computer exercises you will receive sequence data which is not public. You are not allowed to further distribute this data and I ask you to delete copies of the data once the course is finished.
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The Cancer Genome Atlas

 
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R tutorial

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Exome sequencing

R & Bioconductor

 
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  • To install a package see instructions
  • Note: R is already installed on the amc-app1 server
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    • compile code with 'make -f Makefile'
    • download chromosome 1 (fasta file) from the ucsc database and build an index with BWA
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  • SAMtools
    • use bunzip2, tar -xvf and make -f Mafefile to install samtools
 
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  • SAMtools
    • use bunzip2, tar -xvf and make -f Mafefile to install samtools
 
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    • You need to register in order to use this view
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    • You need to register in order to use this viewer
 

Data formats

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Genomes

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Revision 13
10 May 2012 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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    • Tutorial
    • Note: R is already installed on the amc-app1 server
Revision 12
10 Apr 2012 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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Background information

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Next-generation sequencing reviews

 

454 and Solid sequencing technology

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Bias in sequence data

 

RNA-Seq

Exome sequencing

Added:
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>

Bias in sequencing data

 

Tools and data for computer exercises

Important note: for the computer exercises you will receive sequence data which is not public. You are not allowed to further distribute this data and I ask you to delete copies of the data once the course is finished.
Revision 11
06 Apr 2012 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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  • Course material: All course material is provided during the course.
  • ECTS: 6
  • Coordinator: Antoine van Kampen
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Note: This course focuses on the analysis of NGS data. This part of the programme 'bioinformatics' doesn't consider any aspect of GRID (computing).
Revision 10
09 Sep 2011 - Main.AntoineVanKampen
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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Bioinformatics-II: Next Generation Sequencing. RNA-Seq and Exome sequencing

During this bioinformatics programme the participants acquire fundamental skills in Next Generation Sequencing (NGS) and the analysis of NGS data. In particular we will focus on 'exome sequencing' and 'RNA-Seq'.
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  • Location: Science Park and/or Academic Medical Center, Amsterdam. See here how to get there.
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  • Location: Academic Medical Center, Amsterdam. See here how to get there.
 
  • Course material: All course material is provided during the course.
  • ECTS: 6
  • Coordinator: Antoine van Kampen
Revision 9
28 Apr 2011 - Main.AngelaLuijf
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META TOPICPARENT name="EducationBioLab"
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Medical Bioinformatics

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