The rapid development of genomics technology, especially next generation sequencing (NGS), complemented with advanced bioinformatics approaches has revolutionized genomic research. In the past years, a variety of suitable bioinformatics methods to analyse NGS data have been developed and implemented in Backofen lab. In this subproject, we will provide bioinformatics support for next generation sequencing/microarray data for the entire consortium. In order to identify and profile the expression pattern of miRNAs and long RNAs including both mRNAs and lncRNAs, we will provide bioinformatics analysis of small RNA sequencing and RNA-seq, respectively. Furthermore, to complement this analysis, we will also provide tools and pipeline to determine transcription factor binding sites as well as prolife genome wide histone modification patterns from ChIP-seq.
For this purpose, we will setup a data management centre based on Galaxy to provide access to the data generated by the consortium. The Freiburg group is one of the leading Galaxy groups, from the approx. 3000 tools that are available worldwide, more than 500 where added by the Freiburg group. The Freiburger Galaxy server is one of the largest in Germany, with more than 200 users and more than 800 integrated tools. Within this centre, we will provide standardized computational workflows and develop data analysis standards. Furthermore, the centre provides access to the data by the consortium and allows for easy interpretation and visualization. We will also provide training courses for members of the consortium to perform standard analysis task, and will develop specialized workflows for the non-standard tasks in close collaboration with the experimental groups. Rolf Backofen is also the coordinator of the centre of excellence for RNA Bioinformatics, a BMBF funded project (funded by 3.4 Mio € in the next 5 years) that is positively evaluated by the BMBF within the German Network for Bioinformatics, which is a BMBF initiative to improve the bioinformatics service for experimental groups in Germany.