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DATE : JUNE 29
TIME: 13:15 - 16:45
LOCATION: Bern, UniEs Room 105

Now that everyone is gearing up to deal with the large amounts of data generated by the new NextGen Sequencers all accross Switzerland, we would like to call a workshop of the experts to discuss current issues and new ideas.

We set up a mailinglist: deepseq@sympa.systemsx.ch
To join the list, please click here.

Summary

Data Management

We had two presentations:

S Pradervand

An easily deployed sytem for Illumina data managment and samples tracking - slides

M Kohler

openBIS – Deep Sequencing Unit: Current Status and Quality Assessment of Sequencing Data slides

Also the FGCZ has explained what is being used.
Disussion:

  • Which alignment tool is best? It depends on the problem. Everyone uses a different one for different reasons (Bowtie, BWS, Eland, Shrimp, Socs)
  • But the alignment tool not being the same introduces only a small problem, there are bigger issues that need to be understood to keep errors and biases low
  • No silver bullet, experience needed
Data Analysis

J Rougemont

ChIP-seq

Presentation, Discussion:

  • Which protein is where and when in the cell, where proteins bind to DNA, via DNA-protein crosslinking
  • A few hundred bp of DNA are squenced, only tags of length 30-50bp. Then map to the genome.
  • Use MACS for peak finding, see http://genomebiology.com/2008/9/9/R137
Data Visualization

Michael Brudno

SAVANT (please also refer to the SystemsX.ch lecture) This is a publicly available tool

F David, Y Jarosz and M Leleu

Interactive Genome Browser, results viewing software including GenRep, JBrowse, JBrowsOR, GDV, GFeatMiner

E Hunt

VisGenome demo - distort space to fit more information on the screen

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