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Functional Genomics project joined the wiki. E-BioGrid project for biobanking started. We have proudly joined the. 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 . Quality scores histogram from the BGI. Maybe other graphs/data provided by the BGI. Quality scores with the FastqC toolkit. Quality scores per base. Quality scores per . To gain access to restricted area...

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Functional Genomics project joined the wiki. E-BioGrid project for biobanking started. We have proudly joined the. 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 . Quality scores histogram from the BGI. Maybe other graphs/data provided by the BGI. Quality scores with the FastqC toolkit. Quality scores per base. Quality scores per . To gain access to restricted area...

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bbmri | eb-register.com Reviews

https://eb-register.com

Functional Genomics project joined the wiki. E-BioGrid project for biobanking started. We have proudly joined the. 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 . Quality scores histogram from the BGI. Maybe other graphs/data provided by the BGI. Quality scores with the FastqC toolkit. Quality scores per base. Quality scores per . To gain access to restricted area...

INTERNAL PAGES

eb-register.com

1

CoverageAnalysisPipeline – bbmri

http://www.eb-register.com/wiki/CoverageAnalysisPipeline

Antoine van Kampen, Barbera van Schaik, Silvia D Olabarriaga, Mark Santcroos, AMC. Calculates coverage per base. Creates a text file which you can use to make a histogram (coverage versus frequency). SortedBamFile, a sorted bam file. ChromSizesTxt, e.g. the chromInfo.txt from the UCSC database. CoverageHistogram: summary of coveragePerBase. An overview about the genome coverage of the sequence experiment. Load this into excel/calc/gnuplot/some-other-program to make a graph. WF Create BWA index on database.

2

TracGuide – bbmri

http://www.eb-register.com/wiki/TracGuide

The Trac User and Administration Guide. Is meant to serve as a starting point for all documentation regarding Trac usage and development. The guide is a free document, a collaborative effort, and a part of the. It provides an interface to Subversion (and other version control systems), an integrated Wiki and convenient reporting facilities. Using the Wiki subsystem. How to use the built-in Wiki. Reference to the wiki syntax used throughout. Using the Version Control subsystem. Using the Ticket subsystem.

3

Roadmap – bbmri

http://www.eb-register.com/roadmap

Hide milestones with no due date. Minimal SNP and indel calling pipeline. Sep 30, 2010 12:00:00 AM). Have a first pipeline running inspired by Broad. Compare BGI results against known SNP information. For help on using the roadmap. Download in other formats:. Powered by Trac 1.0.7. Visit the Trac open source project at. Http:/ trac.edgewall.org/.

4

GwasQcPipeline – bbmri

http://www.eb-register.com/wiki/GwasQcPipeline

Removed all bad samples (taken from Mathieu). P-link - bfile GvNL 250111 - remove GvNL bad samples.txt - make-bed - out GvNL good samples. P-link - bfile GvNL samples - update-ids GvNL family update.txt - make-bed - out GvNL good fam. P-link - bfile GvNL good fam - update-parents GvNL parents update.txt - make-bed - out GvNL good fam par. Manual check for suspicious individuals (not in trios) and remove them. Check and update sex information. P-link - bfile GvNL good fam par susp - check-sex - make-bed.

5

Imputations – bbmri

http://www.eb-register.com/wiki/Imputations

Working group on Imputation. We have started a working group on imputations to develop a best practice based pipeline that will perform well on the compute resources we will be using. For now the documents are only visible to project members. If you want to get access contact David or Morris. Paul de Bakker (PI). Last modified on Jul 5, 2012 10:35:40 PM. Download in other formats:. Powered by Trac 1.0.7. Visit the Trac open source project at. Http:/ trac.edgewall.org/.

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bbmri

Functional Genomics project joined the wiki. E-BioGrid project for biobanking started. We have proudly joined the. 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 . Quality scores histogram from the BGI. Maybe other graphs/data provided by the BGI. Quality scores with the FastqC toolkit. Quality scores per base. Quality scores per . To gain access to restricted area...

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bbmri

Functional Genomics project joined the wiki. E-BioGrid project for biobanking started. We have proudly joined the. 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 . Quality scores histogram from the BGI. Maybe other graphs/data provided by the BGI. Quality scores with the FastqC toolkit. Quality scores per base. Quality scores per . To gain access to restricted area...

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