wiki:WikiStart

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Functional Genomics project joined the wiki

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e-BioGrid project for biobanking started

We have proudly joined the  e-BioGrid project on a mission to bring nation-wide IT infrastructure for large scale biobanking. First goal is building a model infrastructure for the Dutch Biobank community, BBMRI-NL, that manage ...

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Proposed Quality Control.

Pre-alignment:

  • Duplicate input checking.
  • Quality scores histogram from the BGI.
    • Maybe other graphs/data provided by the BGI.
  • Quality scores with the FastqC toolkit.
    • GC content.
    • Quality scores per base.
    • Quality scores per ...

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  • Posted: 2010-12-14 12:54
  • Author: jlaros
  • Categories: (none)
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Hackathon on pipelines, grid and QC

Yesterday we had a succesfull joint hackathon in Haren accross BBMRI-NL bioinformatics and NBIC biobank and next generation sequencing task forces. Representatives were there from UMCG, AMC, LUMC and NBIC as well as guests of the local genomics coord ...

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  • Posted: 2010-11-30 06:34 (Updated: 2010-11-30 12:25)
  • Author: mswertz
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First raw reads in; Freerk and Morris go to Boston to get GATK running

The first two trio data has been downloaded from BGI. Meanwhile BGI is running the basic analysis, i.e., variant calling on the whole batch. Freerk and Morris went to Boston to learn how to do the same procedure but then using GATK. Hopefully by end ...

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  • Posted: 2010-10-14 23:46 (Updated: 2010-10-17 14:04)
  • Author: mswertz
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BBMRI-NL Rainbow projects:

To gain access to restricted areas please register yourself and then sent login name to:

  • m.a.swertz AT rug.nl or pieter.neerincx AT gmail.com (for RP2)
  • patrickdeelen AT gmail.com or M.H.Moed AT lumc.nl (for RP3)

SOPs and Pipelines:

Using this wiki

As all Wiki pages, this page is editable, this means that you can modify the contents of this page simply by using your web-browser. Simply click on the "Edit this page" link at the bottom of the page. WikiFormatting will give you a detailed description of available Wiki formatting commands.

On top there is menu with additional features

  • Blog - Meetings, events etc can be blogged
  • Roadmap - Overview of the main objectives
  • Tickets - All our TODO's (per roadmap) we can collect under Tickets
  • Browse source - All our scripts we can browsed under Browse Source
  • Subversion - Programmers can commit their code using SVN at  http://gbic.target.rug.nl/bbmri/svn

BBMRI projects are developed in collaboration with

Attachments

Last modified by Rick, 10/09/13 23:58:37 (6 months ago)