Core staff can handle all your bioinformatics needs in next-generation sequence analysis, from data retrieval and management, storage, quality control, analysis and writeup. We follow best practices and re-use public workflows and tools wherever possible, but are happy to adapt existing methods and develop new solutions where required. While we try to offer support in most areas of computational biology HBC’s expertise is focused on two core areas:
1. Next generation sequencing analysis:
Core analysts have extensive experience in managing and analyzing sequencing data, including:
- whole genome and exome sequencing (quality control, mapping, re-alignment, variant calls, prioritization),
- RNA-seq (quantification and de novo transcriptome analysis),
- small RNA-seq (i.e. miRNA analysis),
- single-cell and single-nuclei RNA-seq,
- genome assembly (reference guided and de novo),
- ChIP-seq and ATAC-seq
- bisulfite sequencing
We can also provide support in the design and and analysis of your customized NGS experiment.
2. Functional analysis:
We can provide a path from genes to function by delivering extensive functional annotation, prioritizing new markers and developing testable hypotheses for future experiments. We test for functional information using different gene set enrichment approaches (using Gene Ontology, pathway databases as well as curated and generic gene sets), provide context by integrating your data with public resources such as GEO and TCGA, and explore the biological interaction space in co-expression and high-throughput interaction data sets using network analysis techniques.
3. Grant and manuscript support:
We can support grant proposals and review manuscripts on short notice. The Core’s team has extensive experience in providing standard descriptions and implementing best practices in data management, user and security handling, quality controls and data dissemination to the scientific community that fulfill NIH and NSF requirements and simplify the process of publishing your manuscript. We are available to help you with your data submisison to standardized databases such as the Gene Expression Omnibus and the Short Read Archive.