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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'.

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

Background information

Next-generation sequencing reviews

Sequencing technology


Bias in sequencing data

The Cancer Genome Atlas

Exome sequencing

R & Bioconductor


  • BWA (Burrows-Wheeler Aligner)
    • Manual
    • bz2 file can be unzipped with 'bunzip2 file '
    • tar file can be extracted with tar -xvf file
    • compile code with 'make -f Makefile'
    • download chromosome 1 (fasta file) from the ucsc database and build an index with BWA

  • SAMtools
    • use bunzip2, tar -xvf and make -f Mafefile to install samtools

  • VarScan
    • Documentation
    • make sure to set the program as an executable: chmod a+x
    • Start program from command line with 'java -jar VarScan.v2.2.jar'
    • Use the program 'java -jar VarScan.v2.2.jar pileup2cns'

Data formats

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Topic revision: r15 - 29 Sep 2014, PerryMoerland

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