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Deep Sequencing and a reanalysis of human histone methylation and acetylation patterns.

Werner Van Belle1* - werner@yellowcouch.org, werner.van.belle@gmail.com

1- Yellowcouch;

Abstract :  This talk introduces sequencing by synthesis (sometimes also called solexa sequencing, deep sequencing or digtal gene profiling). This technology has been booming the past few years because it can measure an entire genome expression profile at basepair resolution without predesigned probes. This makes it an excellent explorative tool and depending on the preprocessing of the sample, different information can be obtained. At the cost of a single micro-array one can measure methylation/acetylation patterns, genomic DNA, detect SNP's or measure the transcriptome. Never before has a single experiment, performed in 5 days, yielded 1.5Tb of data and 28'800'000'000 bases. Analyzing this data is a major challenge and the first part of the presentation covers the primary analysis. I will present the acquisition of images, calculation and normalization of intensities, base calling, short fragment quality filtering and how one aligns 800'000'000 short fragments to a genome of choice. The second part of the presentation touches upon some analysis problems and will illustrate our current approach to analyze chip-seq patterns of around 41 humane histone methylations and acetylations tracks. We will also present a major, yet computationally unresolved, challenge in dealing with alignment profiles.

Keywords:  deep sequencing illumina GA pipeline histone methylation and acetylation patterns
Reference:  Werner Van Belle; Deep Sequencing and a reanalysis of human histone methylation and acetylation patterns.; Presented at Brain Research Institute; University of Zürich; Zürich; Switzerland; Switzerland; April 2009
Filesalignment2profile.avi, correlations.avi
See also:
The research article.
The browsable correlation maps between Histone Methylation and Acetylation tracks
Some posters [1, 2, 3]
Presentations of this research at FMI, Novartis, UNIL, University Zürich and ETH Zürich [1, 2]