The Razavi Newman
Integrative Genomics and Bioinformatics Core


Salk Institute for Biological Studies - The Razavi Newman
Integrative Genomics and Bioinformatics Core - Services


The overall goal of IGC is to empower groups at the Salk to leverage genomics in their research. The core can provide advice on experimental design, assist with analysis, or provide training on analysis tools. Due to the diversity of research interests at the Salk and the changing needs of individual labs, the IGC offers a variety of services to help fit specific needs.

Consultation on Experimental Design and Genomics Analysis

Our doors are always open to talk genomics. If you are planning on doing a next-gen sequencing experiment, or just thinking about it, stop by or make an appointment to chat about it. For every scientific question there are several different assays and sequencing technologies available. Making the right decision early on can save time and resources. Likewise, analysis of genomics data can be tricky. The IGC will be more than happy to provide any information or guidance it can to make your project a success.

Standard Data Analysis

For groups that are looking for traditional analysis of common experimental types, IGC offers standard analysis packages. These include mapping data to reference genomes, standard analysis such as peak finding or gene expression calculation, UCSC visualization, and annotation. The end result is a set of analysis files that can be used to get your project started. This includes quality control, and we will be happy to brief you about the results of your experiment and suggest further experiments/analysis that may help advance your work.

Common Analyses Workflows:

  • ChIP-Seq/DamID/ATAC: Mapping, Peak Finding, UCSC files, Motif finding, Annotation, Quality Control
  • RNA-Seq: Mapping, Gene expression calculation, Transcript discovery, Annotation, Quality Control, Differential gene expression testing.
  • DNA-Seq/Regulatory Variant Discovery and annotation.
  • HiC: Mapping, generating contact maps, finding interactions, differential interactions, interaction annotation, visualizing domains and chromatin compartments.
  • RIP-Seq: Quality control, mapping, quantifying RNA abundance and enrichment, generation of tracks for visualization.
  • GRO-Seq: Quality control, mapping, visualization of binding, quantification, annotation.
  • Transcript assembly: genome guided transcript assembly.
  • Miscellaneous Sequence Manipulation, Mapping, Converting formats, etc.

We are working on expanding this list as new tools and pipelines become available.

Advanced Data Analysis

Scientific advancement is often dependent on fully leveraging your data, and for genomics data this can mean developing novel analysis techniques, cross-referencing results with other types of public or private studies, or inventing creative ways to present complex data. This also includes the analysis of cutting-edge or novel techniques for which current analysis approaches are inadequate or unavailable. IGC brings extensive experience analyzing genomics data sets, and was primarily established to help push the envelope on genomics research at the Salk. If your group is looking for expert assistance, come by the IGC or make an appointment and we will be happy to figure out a course of action to fill your needs.


Other services provided by the IGC

  • Data Storage/Archiving/Backup
  • Temporary hosting of data for sharing with collaborators and public servers.
  • Access to shared analysis servers (if you want to try your own basic analysis)
  • Development of interactive analysis tools such as BART and RICK.
  • Developing and hosting interactive data repositories (interactive websites)
  • Help with data submission to public repositories such as GEO

IGC is committed to teaching researchers to perform their own data analysis whenever possible. This involves understanding each of the steps required in the analysis of their data, which software programs are available, and how to use them effectively. This education happens implicitly through each of the services offered through IGC, as well as through online resources such as the IGC wiki and annual bioinformatics and genomics training workshops. In addition, the IGC is dedicated to training the next generation of scientists by providing competitive paid internships for local undergraduates through UCSD AIP and for high school students through the Heithoff-Brody Scholars Program.

Manuscript preparation

Figuring out the best way to present your genomics data in manuscripts or talks can be challenging. There are many different ways to present the data, and researchers new to the field may have trouble choosing the appropriate style of figures. Formatting your data for supplementary tables or submitting sequencing data to public databases like GEO can also be daunting. If you would like help with preparing your manuscript or generating figures, or just need a second opinion on what you did, feel free to contact the IGC.

Grant Writing

IGC is committed to enhancing genomics research at the Salk. Funding for genomics research is an important aspect of this goal, and we are here to help in whatever way we can, including simple advice or the preparation of larger parts of a proposal. Please contact us if you would like some help.