Difference between revisions of "Old Main Page"

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This wiki is meant as a repository for bioinformatical knowledge at the CEES. It is mainly run by Lex, but others are also very welcome to contribute.  
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This wiki is meant as a repository for bioinformatical knowledge at the CEES. It is mainly run by Lex, but others are also very welcome to contribute.
  
*If you want to be able to edit the wiki, let us know and we'll add you to the list of contributors.  
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*If you want to be able to edit the wiki, let us know and we'll add you to the list of contributors.
*If you add a page, please list it below! [[Tips for adding a page|Tips for adding a page]].<br>
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*If you add a page, please list it below! [[Tips for adding a page|Tips for adding a page]].
  
<br>
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== Mailing lists ==
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*'''cees-hpc''': to be used for general information related to the area under /projects/cees, the able CPUs and the cod-nodes. [https://sympa.uio.no/bio.uio.no/subscribe/cees-hpc Subscribe here].
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*'''cod-nodes''': to be used to inform about the other cod-node users about CPUs and memory usage of the cod nodes, aka 'cod-node hugging'&nbsp;:-) USIT will also send emails to that list when discs on the nodes are full etc. [https://sympa.uio.no/bio.uio.no/subscribe/cod-nodes Subscribe here].
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*'''cees-bioinf''': to be used for general information regarding bioinformatics at CEES. [https://sympa.uio.no/bio.uio.no/subscribe/cees-bioinf Subscribe here].
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*[[CEES bioinformatics knowledge|Bioinformatics knowledge present at CEES]]
  
== Mailing lists  ==
 
  
*'''cees-hpc''': to be used for general information related to the area under /projects/cees, the able CPUs and the cod-nodes. [https://sympa.uio.no/bio.uio.no/subscribe/cees-hpc Subscribe here].
 
*'''cod-nodes''': to be used to inform about the other cod-node users about CPUs and memory usage of the cod nodes, aka 'cod-node hugging'&nbsp;:-) USIT will also send emails to that list when discs on the nodes are full etc. [https://sympa.uio.no/bio.uio.no/subscribe/cod-nodes Subscribe here].
 
*'''cees-bioinf''': to be used for general information regarding bioinformatics at CEES. [https://sympa.uio.no/bio.uio.no/subscribe/cees-bioinf Subscribe here].
 
*[[CEES_bioinformatics_knowledge|Bioinformatics knowledge present at CEES]]
 
  
<br>
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== Use of the CEES hardware and Abel ==
  
== Use of the CEES hardware and Abel<br>  ==
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[[Getting access to the cod nodes and Abel|Getting access]]
  
[[User manual cod nodes|User manual cod nodes]]  
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[[User manual cod nodes|User manual cod nodes]]
  
[[Abel use|Abel use]]  
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[[Abel use|Abel use]]
  
[[software_and_modules|Installing software and creating modules]]
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[[Software and modules|Installing software and creating modules]]
  
 
[[Variant calling on Abel]]
 
[[Variant calling on Abel]]
  
<br>
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== Tips, tricks, useful links ==
 
== Tips, tricks, useful links ==
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[[Useful websites with R|Useful websites with R tips and tricks]]
 
[[Useful websites with R|Useful websites with R tips and tricks]]
  
[[Usefull_small_commands_scripts_etc|Usefull small commands/scripts etc in /projects/cees]]
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[[Usefull small commands scripts etc|Usefull small commands/scripts etc in /projects/cees]]
  
 
== How-to's ==
 
== How-to's ==
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[[Submitting to ENA|Submitting sequences to ENA]]
 
[[Submitting to ENA|Submitting sequences to ENA]]
  
[[Using_virtualenv|Using&nbsp;virtualenv on the nodes]]
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[[Using virtualenv|Using&nbsp;virtualenv on the nodes]]
  
 
[[Check insert size distribution new sequencing library|Quickly check the insert size distribution of a new sequencing library]]
 
[[Check insert size distribution new sequencing library|Quickly check the insert size distribution of a new sequencing library]]

Revision as of 11:53, 29 January 2015

This wiki is meant as a repository for bioinformatical knowledge at the CEES. It is mainly run by Lex, but others are also very welcome to contribute.

  • If you want to be able to edit the wiki, let us know and we'll add you to the list of contributors.
  • If you add a page, please list it below! Tips for adding a page.

Mailing lists

  • cees-hpc: to be used for general information related to the area under /projects/cees, the able CPUs and the cod-nodes. Subscribe here.
  • cod-nodes: to be used to inform about the other cod-node users about CPUs and memory usage of the cod nodes, aka 'cod-node hugging' :-) USIT will also send emails to that list when discs on the nodes are full etc. Subscribe here.
  • cees-bioinf: to be used for general information regarding bioinformatics at CEES. Subscribe here.
  • Bioinformatics knowledge present at CEES


Use of the CEES hardware and Abel

Getting access

User manual cod nodes

Abel use

Installing software and creating modules

Variant calling on Abel


Tips, tricks, useful links

Organising your computational work

Useful websites with Unix commands

Useful websites with Python tips and tricks

Useful websites with R tips and tricks

Usefull small commands/scripts etc in /projects/cees

How-to's

PacBio smrtpipe command-line use

Submitting sequences to ENA

Using virtualenv on the nodes

Quickly check the insert size distribution of a new sequencing library

Error correction of Illumina reads using merTrim from the Celera Assembler package

Assembly of Illumina paired end reads using Celera Assembler

File transfer through bioinf3.titan.uio.no