Bioinformatics Services

The Genomics Core at Sanford Consortium, UCSD, offers the following bioinformatics services:

Next-Generation Sequencing (NGS) Analysis

• RNA-Seq: We provide bulk and single-cell RNAseq using standard and custom RNAseq pipelines. You submit the sequence data, and we return gene counts and graphs for reports and publications. Custom analyses are available. 

• Exome Sequencing: Analyze the protein-coding regions of the genome

• Long Read data: Analyze RNA Isoforms, structural variants, and methylation and reconstruct haplotypes. 

• Small RNA-Seq: Identify small RNAs and reveal their role in gene regulation.

• RNA Isoforms: Detect splice variants and explore their functions.

• Somatic Mutation Detection in tumor/normal pairs in cancer research.

• ChIP-Seq: protein-DNA interactions and DNA-associated protein binding sites.

• Re-sequencing and De-novo Assembly of whole genomes.

Data Publication Services

• Data Preparation and Upload to Public Databases: Preparing and uploading large datasets to public databases as required by funding agencies can be laborious. We help with this by offering a data publication service, including data formatting, annotation, and upload to public databases.

Customized Bioinformatics Solutions

• Differential Expression Analysis, correlate gene expression levels with genetic modifications and treatments.

• Variant Calling and Pathway Analysis: Identify SNPs and other variants and correlate them with biological pathways.

• Genomic Data Visualization, advanced graphs of genomic data.

• Custom analysis, statistical analysis,  and experimental design.

• Utilization of Public Annotations and Tracks: Utilize public databases to enhance the interpretation of your data.

• Experienced bioinformaticians for custom analysis, consultations, and support.

The Core is located at Sanford Consortium, UCSD, 2880 Torrey Pines Scenic Dr, Room 1318, La Jolla, CA 92037. 

Bioinformatics service pricing

Consultations are free. Since the projects vary in complexity, we provide individual estimates. A typical RNAseq data analysis costs $450-$900; additional work is charged extra if requested. Please send us a brief description of your needs to Max at mrempel@ucsd.edu or book time on Max's booking page to schedule a complimentary consultation. You can also reach gCore's bioinformatician Anthonius DeBoer, Ph.D., at a2deboer@ucsd.edu.

Where appropriate, please credit SCGM core and  CCBB in your publications.