Genomics & Transcriptomics

We offer training, support and possibilities to collaborate to the FGCZ user for issues in genomics & transcriptomics bioinformatics. Within this field, the main tasks are experimental design, data managment and analysis as well as the implementation and the development of informatics solutions.

Microarray Data Management

All microarray data is managed within B-Fabric. B-Fabric stores raw data and sample annotation and provides automated data analysis pipelines.

Microarray Data Analysis

• We routinely analyse gene expression data with the following software systems/programming environments:

• We support pathway analysis with the MetaCore (GeneGo) web application.

• For a quick analysis of two-channel microarray data, we recommend to make use of the MAGMA web-application.

Next Generation Sequencing Data Analysis

• Standard analysis of 454 data is carried out with Roche 454 GS-FLX Data Analysis Software, which is capable of de novo assembly, whole genome mapping, and amplicon variant analysis.
  
• Analysis of SOLiD data is carried out with open source software from SOLiD Software Development Community.
  
• Application specific data analysis is done using third party software, or through development and implementation of novel algorithms.

Teaching, Support and Collaborations

All FGCZ users with an approved project get basic bioinformatic software and statistics support, which comprises introductory lessons in gene expression data analysis and consulting during experiment planning and data analysis. For projects that need more than standard workflow tools and methods, the FGCZ can support them in the form of collaborations; See also Support Modes > Collaboration.

Contact

Hubert Rehrauer