AMC Graduate School - Bioinformatics Sequence Analysis

Please go the new website: https://bioinformatics.amc.nl/

Links

Schedule and handouts

Monday

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

Tuesday

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

Wednesday

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)

Thursday

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

Friday

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
  • org.Hs.eg.db
  • 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:
source("http://bioconductor.org/biocLite.R")
biocLite(c("DESeq2","edgeR","genefilter","GenomicAlignments","GenomicFeatures","gplots","org.Hs.eg.db","parathyroidSE","RColorBrewer","Rsamtools","rtracklayer"))

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
 

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