Difference: MikSeminarsExomeExercises (1 vs. 5)

Revision 5
07 Jan 2013 - Main.PerryMoerland
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META TOPICPARENT name="EducationMIKSeminars2012"
Medical Bioinformatics

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Data

Exome data for 4 Nicolaides-Baraitser patients will be provided to you as part of the SARA HPC Cloud

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Unix tutorial

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UNIX

 
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R tutorial

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R

 
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    • 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'
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    • Note: VarScan is already pre-installed in the SARA HPC Cloud.
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    • Note: VarScan is already pre-installed in the SARA HPC Cloud.
 

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    • Note: AnnoVar is already pre-installed in the SARA HPC Cloud.
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    • Note: AnnoVar is already pre-installed in the SARA HPC Cloud.
 

  • SAMtools
    • use bunzip2, tar -xvf and make -f Mafefile to install samtools
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    • Note: SamTools is already pre-installed in the SARA HPC Cloud.
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    • Note: SamTools is already pre-installed in the SARA HPC Cloud.
 

Revision 4
07 Jan 2013 - Main.BarberaVanSchaik
Line: 1 to 1
 
META TOPICPARENT name="EducationMIKSeminars2012"
Medical Bioinformatics

Line: 11 to 11
 

Exome sequencing in practice

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  • The links provided below can be used during the computer exercises.
  • Links to R and Unix tutorials are provided but not required to perform the computer exercises. Nevertheless, if you are interested and have the time you can have a look at these tutorials as well.
Revision 3
07 Jan 2013 - Main.PerryMoerland
Line: 1 to 1
 
META TOPICPARENT name="EducationMIKSeminars2012"
Medical Bioinformatics

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BackSort
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BackSort
 

Line: 15 to 15
 
  • The links provided below can be used during the computer exercises.
  • Links to R and Unix tutorials are provided but not required to perform the computer exercises. Nevertheless, if you are interested and have the time you can have a look at these tutorials as well.
Changed:
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<

VirtualBox: software and data

Note: instructions for installation are provided only in case you want to install these tools on your own computer. All tools that are required for the computer exercises are pre-installed in a VirtualBox that will be provided to you on a USB stick
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SARA HPC Cloud: software

Note: instructions for installation are provided below only in case you want to install these tools on your own computer. All tools that are required for the computer exercises are pre-installed in the SARA HPC Cloud. An IP number, login name and password will be provided to you.
 

Data

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Exome data for 4 Nicolaides-Baraitser patients will be provided to you as part of a VirtualBox on a USB stick.
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Exome data for 4 Nicolaides-Baraitser patients will be provided to you as part of the SARA HPC Cloud
 

Unix tutorial

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  • Note: R and the required packages are already pre-installed in the SARA HPC Cloud.
 

Tools

  • BWA (Burrows-Wheeler Aligner)
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    • bz2 file can be unzipped with 'bunzip2 file '
    • tar file can be extracted with tar -xvf file
    • compile code with 'make -f Makefile'
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    • download chromosome 2 (fasta file) from the ucsc database
    • Note: BWA and the reference sequence for chromosome 2 are already pre-installed in the provided VirtualBox.
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    • download chromosome 9 (fasta file) from the UCSC database
    • Note: BWA and the reference sequence for chromosome 9 are already pre-installed in the SARA HPC Cloud.
 

Line: 51 to 48
 
    • 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'
Changed:
<
<
>
>
    • Note: VarScan is already pre-installed in the SARA HPC Cloud.
 

Changed:
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<
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    • Note: AnnoVar is already pre-installed in the SARA HPC Cloud.
 

  • SAMtools
    • use bunzip2, tar -xvf and make -f Mafefile to install samtools
Changed:
<
<
>
>
    • Note: SamTools is already pre-installed in the SARA HPC Cloud.
 
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Data formats

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  • Data formats
 
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Genomes

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  • Human genome
 
Revision 2
20 Jan 2012 - Main.AntoineVanKampen
Line: 1 to 1
 
META TOPICPARENT name="EducationMIKSeminars2012"
Medical Bioinformatics

Line: 10 to 10
  -->
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Tools and data for computer exercises

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Exome sequencing in practice

  • Document with computer exercises: document (docx)
  • The links provided below can be used during the computer exercises.
  • Links to R and Unix tutorials are provided but not required to perform the computer exercises. Nevertheless, if you are interested and have the time you can have a look at these tutorials as well.

VirtualBox: software and data

  Note: instructions for installation are provided only in case you want to install these tools on your own computer. All tools that are required for the computer exercises are pre-installed in a VirtualBox that will be provided to you on a USB stick

Data

 
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