Welcome to GOPHER’s documentation!

Contents

• Installing and running GOPHER
  • Requirements
  • Using the pre-built GOPHER app
  • Building GOPHER from source
  • Running GOPHER
• GUI – Data preparation
  • Overview
  • Choosing a genome build
  • Choosing enrichment targets
• GUI – Design setup
  • Overview
  • Choosing the viewpoint design
  • Choosing restriction enzymes
  • Miscellaneous parmeters
  • Bait size
  • Margin size
  • Unbalanced margins?
  • Creating viewpoints
• GUI – Viewpoint window
  • Analysis window
  • Editing viewpoints
  • Zooming out and in
  • UCSC genome browser link
• Exporting results
  • Exporting BED file
  • Building the regulatory exome
  • Digest file export
  • Exporting the project file
• Concepts and terminology
  • Introduction to Capture Hi-C
  • Approaches to viewpoint design
  • Usable baits
  • Balanced and unbalanced margins
• Probe upload
  • Export of probes from GOPHER
  • Upload to Agilent’s SureDesign wizard
  • Upload to other providers
• Troubleshooting
  • Connection issues
  • Proxy
  • Java version
  • Memory errors
  • Logging

GOPHER

GOPHER (Generator Of Probes for capture Hi-C Experiments at high Resolution) is a Java application that helps users design enrichment probes for capture Hi-C and related protocols. Capture Hi-C (CHC) is based on the Hi-C protocol but uses capture baits (similar to whole-exome sequencing) to enrich a set of viewpoints. Commonly, the viewpoints represent proximal promoter regions (surrounding the transcription start site; TSS) of genes of interest or of all protein-coding genes.

CHC detects interactions between viewpoint regions and distal enhancers (or other genomic regions). CHC has been most commonly performed with the 4-cutter DpnII or with the 6-cutter HindIII.

GOPHER requires Java 8 or higher to run. The source code of GOPHER can be downloaded from the GOPHER GitHub repository (https://github.com/TheJacksonLaboratory/Gopher/), but most users will want to download the pre-compiled application from the Releases page at https://github.com/TheJacksonLaboratory/Gopher/releases. If desired, the application can be easily built from source using maven.

Currently, GOPHER supports design of probes for human (GRCh37, GRCh38) and mouse (mm9, mm10). The application guides users through the process of downloading genome and transcript data from the UCSC Genome Browser; GOPHER uses this data to determine the locations of restriction sites and TSS for the chosen genes. Following this, the user can upload a list of gene symbols and choose a restriction enzyme. The application will then generate a list of suggested viewpoints according to a simple or extended approach. The user can visualize the viewpoints and selected restriction fragments within their genomic context directly in the GOPHER application, and can select or deselect fragments. Finally, the user can export a BED file with the chosen fragments that can be used to design probes (often in conjunction with a Wizard of a manufacturer). Additionally, a file with URLs for the UCSC browser is provided so that the user can inspect the data in the UCSC Genome Browser before proceding with the experiment.

This site provides detailed explanations and tips for the various steps of this procedure.