Difference: NBIC_RNA-seq (1 vs. 14)

Revision 14
16 Oct 2015 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
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NBIC Advanded RNA-seq Course 2012

Revision 13
29 Sep 2014 - Main.PerryMoerland
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META TOPICPARENT name="EducationBioLab"
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Medical Bioinformatics

 
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Revision 12
14 Oct 2012 - Main.AntoineVanKampen
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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NBIC Advanded RNA-seq Course 2012

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NBIC Advanded RNA-seq Course 2011

Revision 11
10 Oct 2012 - Main.AntoineVanKampen
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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NBIC Advanded RNA-seq Course

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NBIC Advanded RNA-seq Course 2012

NBIC Advanded RNA-seq Course 2011

 
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Schedule

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Schedule

 
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Handouts

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Handouts

 
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Getting started

  • Start Winscp and connect to www.bioinformaticslaboratory.nl
  • Copy this file to your home directory on the server.
  • Start Xming and putty (enable x11 forwarding).

Data

  • De input data can be read (do not copy) from the home directory of stud00, e.g. > samtools view ~stud00/data/Marieke/bn1_chr10.bam > bn1_chr10.sam
  \ No newline at end of file
Revision 10
19 Sep 2011 - Main.BarberaVanSchaik
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META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

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Getting started

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  • Windows login: bioinfo bioinfo
  • Start Winscp and connect to www.bioinformaticslaboratory.nl (stud01-stud30 oGh9Eideim).
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  • Start Winscp and connect to www.bioinformaticslaboratory.nl
 
  • Copy this file to your home directory on the server.
  • Start Xming and putty (enable x11 forwarding).
Revision 9
25 Aug 2011 - Main.AntoineVanKampen
Revision 8
24 Aug 2011 - Main.MarcelWillemsen
Line: 1 to 1
 
META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

Line: 13 to 13
 

Schedule

Added:
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Handouts

 

Getting started

  • Windows login: bioinfo bioinfo
  • Start Winscp and connect to www.bioinformaticslaboratory.nl (stud01-stud30 oGh9Eideim).
Revision 7
24 Aug 2011 - Main.MarcelWillemsen
Line: 1 to 1
 
META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

Line: 21 to 21
 

Data

Deleted:
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  • De input data can be read (do not copy) from the home directory of stud00, e.g. read.csv("~stud00/data/input_file.csv")
  \ No newline at end of file
Added:
>
>
  • De input data can be read (do not copy) from the home directory of stud00, e.g. > samtools view ~stud00/data/Marieke/bn1_chr10.bam > bn1_chr10.sam
  \ No newline at end of file
Revision 6
23 Aug 2011 - Main.MarcelWillemsen
Line: 1 to 1
 
META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

Line: 14 to 14
 

Getting started

Changed:
<
<
  • Start Winscp and connect to www.bioinformaticslaboratory.nl (stud00-stud30 oGh9Eideim).
>
>
  • Windows login: bioinfo bioinfo
  • Start Winscp and connect to www.bioinformaticslaboratory.nl (stud01-stud30 oGh9Eideim).
 
  • Copy this file to your home directory on the server.
  • Start Xming and putty (enable x11 forwarding).
Revision 5
22 Aug 2011 - Main.MarcelWillemsen
Line: 1 to 1
 
META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

Line: 16 to 16
 

Getting started

  • Start Winscp and connect to www.bioinformaticslaboratory.nl (stud00-stud30 oGh9Eideim).
  • Copy this file to your home directory on the server.
Changed:
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  • Start putty.
>
>
  • Start Xming and putty (enable x11 forwarding).
 

Data

Revision 4
22 Aug 2011 - Main.MarcelWillemsen
Line: 1 to 1
 
META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

Line: 13 to 13
 

Schedule

Changed:
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<

Data

>
>

Getting started

  • Start Winscp and connect to www.bioinformaticslaboratory.nl (stud00-stud30 oGh9Eideim).
  • Copy this file to your home directory on the server.
  • Start putty.
 
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>

Data

 
Changed:
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<

Getting started

export SAMTOOLS=/data/programs/samtools-0.1.17
export TOPHAT=/data/programs/tophat-1.3.1.Linux_x86_64
export BOWTIE=/data/programs/bowtie-0.12.7
export BEDTOOLS=/data/programs/BEDTools-Version-2.12.0/bin
export PATH=$BEDTOOLS:$TOPHAT:$SAMTOOLS:$BOWTIE:$PATH
>
>
  • De input data can be read (do not copy) from the home directory of stud00, e.g. read.csv("~stud00/data/input_file.csv")
Revision 3
18 Aug 2011 - Main.MarcelWillemsen
Line: 1 to 1
 
META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

Line: 13 to 13
 

Schedule

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Course material

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Data

 

\ No newline at end of file
Added:
>
>

Getting started

export SAMTOOLS=/data/programs/samtools-0.1.17
export TOPHAT=/data/programs/tophat-1.3.1.Linux_x86_64
export BOWTIE=/data/programs/bowtie-0.12.7
export BEDTOOLS=/data/programs/BEDTools-Version-2.12.0/bin
export PATH=$BEDTOOLS:$TOPHAT:$SAMTOOLS:$BOWTIE:$PATH
Revision 2
18 Aug 2011 - Main.MarcelWillemsen
Line: 1 to 1
 
META TOPICPARENT name="EducationBioLab"
Medical Bioinformatics

Line: 8 to 8
 
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Advanded RNA-seq Course

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NBIC Advanded RNA-seq Course

 

Schedule

 
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