Bioinformatics and Omics data science
ManagementProf. Dr. Marek Bartkuhn |
Contact InformationProf. Dr. Marek Bartkuhn |
Description
The Bioinformatics Core Facility of the Medical Faculty of the Justus-Liebig-University Giessen is located within the Institute for Biomedical Informatics and Systems Medicine. We support scientific projects in the analysis of complex data sets derived from Omics-experiments, especially in the context of NGS-based approaches like transcriptome, epigenome or genome sequencing. We process raw sequencing reads and perform high-level analyses to provide meaningful biological interpretations of Omics studies including the generation of figures for publication. Datasets from multiple modalities may also be analyzed in an integrative manner. We also train interested PhD candidates and postdocs in these methods. Furthermore, we provide access to compute infrastructure for projects that cannot be computed on conventional laptops or desktop PCs.
The core facility is open to collaborations with all groups of the JLU and external institutions. It is directed by Prof. Dr. Marek Bartkuhn. For detailed information and guidelines on data submission and costs, you can contact the core facility via email or phone.
Instrumentation/Software
We are operating on standard Linux servers with appropriate storage, memory and CPU for handling of large datasets. In cases that exceed the local resources we are collaborating with the Bioinformatics Core Facility (BCF) of Prof. Dr. Alexander Goesmann or make use of IT infrastructure provided through the deNBI initiative (German Network for Bioinformatics Infrastructure). We solely use open source software developed from the public domain like R, RStudio, BioConductor packages, Python and bioinformatics packages like Scanpy and many more.
Services
We provide analysis for several modalities including integrative analysis when multiple modalities are studied within the same project.
Transcriptome assays:
RNA-seq: quality control, filtering and mapping of reads, counting of gene specific reads, filtering/quality control, dimensionality reduction, clustering, detection of differentially expressed genes, over-representation analysis, gene set enrichment analysis, weighted correlation network analysis and many others upon request, comparison to public data sets, upload to public databases (GEO, ArrayExpress etc.), analysis of alternative splicing events
Metabolic labelling of nascent RNA (SLAM-seq, 5EU-seq and others): as above, inference of synthesis, degradation of processing rates
scRNA-seq: quality control, filtering and mapping of reads, counting of gene specific reads, filtering/quality control, dimensionality reduction, clustering, detection of differentially expressed genes, celltype annotation, pseudo-time analysis, velocity analysis, inference of cell-cell communication, over-representation analysis, gene set enrichment analysis, weighted correlation network analysis and many others upon request, comparison to public data sets, upload to public databases (GEO, ArrayExpress etc.)
Epigenomic assays:
ChIP-seq/ CUT&RUN/ CUT&TAG: quality control, filtering and mapping of reads, peak detection, peak annotation, comparison to other binding or gene expression datasets, differential peak detection, over-representation analysis, gene set enrichment analysis and many others upon request, comparison to public data sets, upload to public databases (GEO, ArrayExpress etc.)
Genomic assays:
Genome re-sequencing (WGS / Exome / Panel): quality control, filtering and mapping of reads, detection of genomic variations like SNVs in somatic and germline context
We also perform analysis of data derived from alternative experimental approaches upon request.
Counseling and training:
Moreover, we provide training of above mentioned methods for interested PhD candidates and postdocs in these methods.
Access to computational infrastructure:
Furthermore we provide access to compute infrastructure for projects that cannot be computed on conventional laptops or desktop PCs. Virtual machines hosted on our servers can accessed via web interfaces without the requirement for specific IT infrastructure.
Downloads/Links:
Bioinformatics Core Facility specific user regulations.