The analysis of data that transforms high-throughput raw data into biologically meaningful information can present a challenge to clinical, translational, and basic researchers alike. The CRI Bioinformatics Core offers services and expertise designed to allow BSD investigators to take full advantage of high-throughput technologies.

 View a selection of publications partially made possible by our bioinformatics analysis work.

SERVICES

 

  • Bioinformatics analysis of high-throughput biological data using our well-defined analysis pipelines
  • Consulting services for custom analysis beyond our standard pipelines, including proteomics and genome-wide association studies
  • Grant writing assistance, including assistance fully developing the bioinformatics components of a grant, cost analysis, letters of support, and documenting the availability of tools and expertise to complete the research indicated
  • A growing training program that includes free monthly seminars in bioinformatics topics–visit Bioinformatics Training for details

METHODOLOGY

 

The Bioinformatics Core’s work combines the use of powerful computing resources, advanced analytics tools, and a commitment to security to transform large amounts of raw data into meaningful results. We use the CRI’s high-performance computing cluster and large-scale storage resources, with which complex analytics can be executed in parallel or distributed environments to produce fast data processing rates, improving application performance and cost effectiveness. Through advanced high-throughput analytics solutions, we dig down to the root of each computational challenge and design the most direct path to a solution. All our work is protected with the CRI’s automated, resilient backup and security systems, ensuring data integrity and access controls that are aligned with standards required by HIPAA, FISMA, and other regulations.

LET’S GET STARTED

 

Planning an experiment? The Bioinformatics Core has created a guide to Bioinformatics Experimental Design to help you get the best results.

For each project request, the Core creates a proposal for the researcher that includes the scope of deliverables, a timeline for completion, and the estimated cost. The execution of the project is guided by frequent discussion between researchers and bioinformaticians, with progress updates provided regularly. Project results are delivered in the form of a written report.

BEGIN A PROJECT

Questions? Email us here.
Have you worked with us before? We’d love your feedback.

 ANALYSIS PIPELINES

The following bioinformatics pipelines are currently available.

Illumina

  • RNA-Seq: Raw Data QC, Filtering, Mapping, Data Summarization, Expression Quantification, Differentially Expressed Genes, Pathways, and Gene Ontology Analysis
  • ChIP-Seq: Raw Data QC, Filtering, Mapping, Peak Calling, Peak Differential Analysis, Peak Related Genes Analysis, Gene Ontology Analysis, and Annotation
  • Exome Sequencing: Raw Data QC, Pre-processing, Mapping with 3 different tools, Realignment and Quality Recalibration, Multiple Samples Variant Calling, Variant Annotation, Varian Comparison, Filtration, and Summarization
  • Whole Genome Re-Sequencing (WGRS): Raw Data QC, Filtering, Mapping, Genotyping, SNP Detection, InDel Detection, SV (Somatic SV) Detection, CNV Analysis, and Annotation
  • Consensus Genotyping Pipeline: Genotyping, SNP Detection and InDel Detection using three different methods (Samtools, GATK and Atlas-2), comparison of variant calls, list of consensus call variants, and list of method specific calls
  • De-novo Assembly: Raw data QC, Merging, Clipping, Filtering, Contigs Assemble, Scaffold Assembly, Assemble Statistics, and Downstream Analysis
  • Somatic Mutation Detection for Tumor/Normal Pairs: Raw Data QC, Pre-processing, Mapping with 2 different tools, Realignment and Quality Recalibration, Somatic Mutation Detection with 4 different tools, Variant Annotation, and Summarization
  • Small RNA-Seq: Raw Data QC, Filtering, Mapping, Data Summarization, Quantification, Detection of Differentially Expressed miRNAs, Putative Gene Target Prediction, and Pathways Analysis

SOLiD

  • RNA-Seq: Raw Data QC, Filtering, Mapping, Data Summarization, Expression Quantification, Differentially Expressed Genes, Pathways, and Gene Ontology Analysis
  • Whole Genome Re-Sequencing (WGRS): Raw Data QC, Filtering, Mapping, Genotyping, SNP Detection, InDel Detection, SV (Somatic SV) Detection, CNV Analysis, and Annotation
  • ChIP-seq: Raw Data QC, Filtering, Mapping, Peak Calling, Peak Differential Analysis, Peak Related Genes Analysis, Gene Ontology Analysis, and Annotation
  • De-novo Assembly: Raw Data QC, Merging, Clipping, Filtering, Contigs Assemble, Scaffold Assembly, Assemble Statistics, and Downstream Analysis

Illumina and Affymetrix Expression Arrays

  • Filtering, Data Summarization and Normalization, Sample/Gene/Probe-based QC, Differentially Expressed Genes, Functional Annotation, and Pathway Enrichment Analysis

Affymetrix and Exiqon miRNA Arrays

  • Filtering, Data Summarization and Normalization, Sample/Gene/Probe-based QC, Differentially Expressed miRNAs, Predict miRNA Targeted Genes, Functional Annotation, and Pathway Enrichment Analysis

We also offer custom-made pipelines and expertise for types of analysis not listed above, including proteomics and genome-wide association studies. Email us to get started!

  TOOLS AND DATASETS

The Bioinformatics Core maintains the following catalogs of software tools, reference datasets, and databases for use by the BSD research community: