Analytical Services

Consultations

• Your initial 30-minute consultation is free
• An estimate of anticipated costs will be provided to investigators prior to initiation of work
• Grant writing or editing requests and manuscript revisions will be subject to recharge
• Please fill out a consultation request form and we will contact you to schedule a meeting

CCBB office hours

Beginning May 2023, CCBB will host in-person office hours, to provide a space for informal consultation, project planning, or other questions. Please contact Brin Rosenthal () before stopping by, as our schedules are subject to change. The schedule and location may be found here.

Rates

Effective January 1, 2022: To allow us to continue to serve the UCSD faculty at a heavily subsidized rate made possible by the VCHS and ACTRI, an operational charge will be applied at project start and after every 120 hours. Please contact Dr. Brin Rosenthal, Associate Director for Research of CCBB, if you have any questions.

Analytical Services

Please allow one business day for an initial response.

• Transcriptomics (RNA-Seq, miRNA-Seq, microarrays, single-cell RNA-Seq) Study design, alignment, gene-level or transcript level quantification, differentially expressed gene lists, gene set annotation, genome visualization, network analysis

• Genomics (Exome / Whole Genome Sequencing, SNP arrays, GWAS) Study design, alignment, SNPs, indels, CNVs, structural variants, annotation, genome visualization, germline or somatic mutation calls, network analysis

• Epigenomics (ChIP-Seq, ATAC-Seq, methylation arrays, Bisulfite-Seq) Study design, alignment, peak calling, visualization, comparative analysis, motif search, integration with RNA data (optional), differential methylation, network analysis

• Other available analyses:
  • Metagenomics/microbiome (16S rRNA-Seq, shotgun sequencing) Study design, OTU picking, taxonomic abundance identification, alpha and beta diversity evaluation, network analysis
  • Single-cell Multiomics (ATAC-Seq and RNA-Seq)
  • CRISPR screens (single, dual screens)
  • Network Analysis Protein-protein interactions, network propagation, data integration, subnetwork identification
  • Custom Analytical Pipelines & Algorithm Development Novel algorithms, custom analytical pipelines, code refactoring, custom integrative analyses
  • Manuscript preparation: Provide ongoing support for drafting and revising manuscript text, figures, and methods. Scoped per project with a dedicated monthly budget.

Data storage and transfer services

Estimates below are shown for the UCSD internal rate. All projects are subject to operational charges as listed above.

Data storage

• CCBB offers data storage on Amazon AWS S3 for $500 for 3 years.

Alternatively, we offer CCBB help with set-up of new PI AWS account. Includes data transfer to new account. No ongoing support provided after transfer. $900

GEO upload

CCBB offers a GEO data upload service, including preparing required files and metadata:

• If CCBB does not already store the data and metadata: $2160-$4320
• If CCBB stores data and metadata: $2160

Additional Services

• Custom analytical pipelines/algorithm development
• Grant consultations: please provide as much notice as possible if you require assistance writing a custom section for a grant proposal
• Personalized training & tutoring
• Long-term collaborations: Please email for more information

CTRI Affiliates

UC San Diego Altman Clinical and Translational Research Institute (ACTRI) is pleased to announce the addition of a new Vouchers category to support Center for Computational Biology and Bioinformatics (CCBB) services. This new level of support for CCBB includes three funding tiers, ranging from $500 to $10,000.