Registration for deep sequencing data analysis course
April 14-16, 2009 in Biomedicum Helsinki (Haartmaninkatu 8, 00290 Helsinki)
The large amounts of data derived from next generation sequencing projects makes efficient data mining strategies necessary. During the course you will learn strategies for the analysis of mRNA-Seq data as well analysis pipelines for ChIP-Seq. These strategies include
• high efficiency mapping of raw sequence tags
• clustering of sequence tags
• data integration into up to date genome annotation
• downstream analysis of tag covered regions.
The course is based on real world examples. We will show the possibilities for extending genome annotation, splice variant detection and discovery of new transcriptional units. In addition the down stream biological mining of enriched regions from ChIP-Seq will be demonstrated. This will focus on transcription factor (TF) analysis in terms of TF overrepresentation in enriched regions and the discovery of functional motifs and patterns of TFs. New insights into biological mechanisms can be gained by overlaying data from different experiment types.
The course is meant for students/postdocs/senior scientists interested in bioinformatic data analysis of deep sequencing data produced using Roche 454 / Illumina Solexa/ ABI SOLiD sequencers. The course will concentrate on the Genomatix (www.genomatix.de) Genome Analyzer software. Applications for DNA-seq, mRNA-seq, miRNA-seq, and ChIP-seq will be introduced.
The course program is as follows:
April 14:
- A brief overview of 454 / Solexa / SOLiD systems
- presentations by the course participants introducing their own projects
April 15:
Introduction to the Genomatix NGS analysis pipeline - methodological background
Demo and hands-on analysis examples for ChIP-Seq and RNA-Seq:
- mapping
- SNP detection
- splice junction detection
- clustering (peak detection)
- expression analysis
- read and cluster classification
- analysis of overrepresented TF binding sites and modules
- definition of new common sequence motifs in ChIP regions
- next-neighbor analysis of ChIP regions
- TFBS framework analysis of ChIP regions
- meta analysis: positional correlation of different data sets and genomic annotation
- visualization in genome browser
April 16:
- Participants have an opportunity to analyze their own sequencing data
On April 15 and 16, training is conducted by the Genomatix experts.
In order to register, please fill in the electronic form below. Number of participants is limited to 20. Priviledge is given to those students who already have their own data to analyze. Students will be able to receive credits from the course, in which case a presentation on April 14 is mandatory.
Registration fee is 250 €. HBGS, VGSB, and GSBM graduate schools will cover the fee of their own students.
Registration deadline is on March 31 and information concerning the approved applicants is emailed by April 6.
Additional information is available from
Dario Greco (dario.greco@helsinki.fi)
Iiris Hovatta (iiris.hovatta@helsinki.fi)
Outi Monni (outi.monni@helsinki.fi)
Petri Auvinen (petri.auvinen@helsinki.fi)