The Razavi Newman
Integrative Genomics and Bioinformatics Core

Tutorials

Please check out the IGC wiki for additional information on the core and genomics analysis. Our 2017 workshop website has additional slides and information on basic genomics analyses, and we also encourage you to check out these valuable resources on next-gen sequencing and genomics analysis:

• HOMER next-generation sequencing tutorial
• Linux Command Reference
• RNA-Seq Best Practices
• Importance of Biological Replicates
• Replicates vs Sequencing Depth
• Comparison of popular differential expression tools
• What are the tools available for isoform level expression analysis?
• ChIPSeq Design and Analysis Overview
• Original HiC Paper by Lieberman-Aiden et al. (2009)
• 4D Nucleome Project Tools

Analysis Tools

There are many tools to help you analyze data. We have many command-line tools installed on our shared servers, and there are many online tools available so please contact us if you have specific questions. Here are some of our favorites:

• UCSC Genome Browser is a powerful online visualization tool for all of your linear genomics datasets.
• GSEA: Gene Set Enrichment Analysis is used to find gene set enrichment signatures in your gene datasets.
• WebGestalt: Web-based Gene Set Analysis Toolkit is also used to check if there are pathways or GO terms enriched in your gene lists.
• RICK: RNA Interactive Computing Kit for automated RNA-Seq analysis from a raw count table.
• BART: Bioinformatics Array Research Tool for automated microarray analysis.

Sequencing

IGC is not a sequencing core. The current focus of IGC is the analysis of genomics data. The NGS core is responsible for the generation of next-gen sequencing data, including library preparation, quantification, and actual sequencing (http://ngs.salk.edu/). However, IGC can help advise groups on their options and coordinate sequencing efforts between multiple groups to help minimize costs.

IGC can offer advice on experimental design, including selection of the appropriate genomics assays, library prep protocols, and sequencing strategies. If your group is new to sequencing, it is a good idea to talk about your plans ahead of time to understand what options are available and to make sure your sequencing plans match the type of data analysis you hope to accomplish after getting your data back.

IT help

The IGC works closely with the NGS core and the Salk IT department to ensure that all computational resources and data are maintained properly. If you lost your sequencing data link, or need to verify sequencing details please contact the NGS core. If you are having trouble running bioinformatics analyses or have issues with bioinformatics-related tools, please contact the IGC. If you are having trouble reaching a server, need help with the Salk VPN, or are having general issues with your computer, email, or phones, please contact the Salk IT.