AMC Graduate School - Bioinformatics Sequence Analysis

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Schedule and handouts


Type Subject Teacher Material
Lecture Introduction Barbera van Schaik slides (pdf)
Lecture Sequencing techniques Marja Jakobs  
Computer practicum Introduction Aldo Jongejan exercises (doc) , C3ND


Type SubjectSorted ascending Teacher Material
Lecture Data pre-processing Barbera van Schaik
Computer practicum Galaxy sequence alignment Barbera van Schaik
Lecture Multiple sequence and NGS alignment Barbera van Schaik
Lecture/workshop Pairwise sequence alignment Barbera van Schaik


Type Subject Teacher Material
Lecture Gene finding Antoine van Kampen slides (pptx)
Case Neuroblastoma Jan Koster  
Computer practicum Introduction into R2: Genomics Analysis Piet Molenaar and Jan Koster  
Computer practicum Introduction Unix and R self study Command-line bootcamp, Intro R (pdf), Intro unix (doc)


Type Subject Teacher Material
Lecture Exome sequencing Antoine van Kampen slides slides(pptx)
Computer practicum Exome sequencing I Antoine, Barbera see below
Computer practicum Exome sequencing II Antoine, Barbera see below


Type Subject Teacher Material
Lecture RNA sequencing Perry Moerland slides
Computer practicum RNA sequencing Perry, Aldo exercises, solutions, R code, R object (Section 3.2)
Case Immunology Paul Klarenbeek slides

List of R/Bioconductor packages:

  • DESeq2
  • edgeR
  • genefilter
  • GenomicAlignments
  • GenomicFeatures
  • gplots
  • parathyroidSE
  • RColorBrewer
  • Rsamtools
  • rtracklayer

This is how you can install the R packages that are used in these exercises on your own computer. Start R, and type this in the console:

Computer exercises 'Exome sequencing'

For these exercises you will need access to the Cloud. An IP number, login name and password will be provided to you

  • Exercises:
    • See handouts or 'Documents' below.

  • Documents
    • User manual of the Linux 'pico' editor
    • Excel file with all variants found in four patients with Nicolaides-Baraitser syndrome
    • R script with to implement your filtering strategy.

Topic revision: r42 - 12 Mar 2018, UnknownUser Search
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