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Consulting Bioinformatics & Bioinformatics Services

Our company is highly experienced in the analysis of NGS data from common sequencing platforms including colour space data, paired and single-end data. We offer bioinformatics services with flexible statistical tools for quality control, visualization, and high level analysis taking your analysis far beyond the level achieved by standard NGS software. Our team of interdisciplinary experts develops custom-tailored solutions for your specific research questions, covering the detection of protein binding regions on DNA (e.g. ChIP-Seq, MeDIP-Seq) as well as mutations (SNPs, InDels, CNV) and expression analyses (RNA-Seq, DGE).

We offer:

Consultation on experiment and study design
Optimization of analysis workflows
Result display with methods of scientific visualization
Programming of specific analysis tools
 

We are specialized in:

General NGS processing including

Quality control
Trimming of adapters, primers, bad quality bases
Read mapping to reference genome


Different experiment types:

ChIP-Seq (TFs, histone modifications, methylations):
Peak calling
Differential analysis of different TFs, cell lines, organisms


RNA-Seq:
Splice junction mapping
Gene expression analysis (coding genes, miRNA, and ncRNA),
Differential analysis of different treatments, patients, cell lines, organisms comparing two or more states


DNA-Seq:
SNP and InDel calling in targeted sequencing, Exome-Seq, and whole genome sequencing experiments,
Assembly of small genomes (bacteria, virus, phage, …)


Downstream analysis of for the above-mentioned experiments depending on problem of interest:
Annotation of results (e.g. Ensembl, RefSeq, GENCODE, dbSNP)
Motif search (e.g. MEME, DREME)
Gene set enrichment analysis for identification of functional pathways and Gene Ontology terms
Visualization of results with interactive HTML tables containing links to relevant resources (e.g. Ensembl, USCS genome browser, dbSNP) and connected to the IGV genome browser


Integrative analysis of different types:
comparing RNA-Seq and ChIP-Seq results
comparison of different organisms (e.g. human vs. mouse)

For customers with specific questions, adapted methods and algorithms can be implemented.

For more information please contact the corresponding department using our contact form.