TERRA-REF Documentation
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  • Introduction
  • Data Sources
  • Software
  • Scientific Objectives and Experimental Design
    • Protocols
      • Controlled Environment Protocols
      • Manual Field Data Protocols
      • Phenotractor Protocols
      • Sensor Calibration
      • Template Protocol
      • UAV Protocols
    • Experimental Design
      • Experimental Design Danforth
        • Sorghum Lines Danforth
      • Experimental Design Genomics
        • Sorghum Lines Genomics Year 1
        • Sorghum Lines Genomics Year 1 (continued)
        • Sorghum Lines Genomics Year 2
      • Experimental Design MAC
  • User Manual
    • What Data is Available
    • Data Products
      • Environmental conditions
      • Fluorescence intensity imaging
      • Genomics data
      • Geospatial information
      • Hyperspectral imaging data
      • Infrared heat imaging data
      • Multispectral imaging data
      • Meteorological data
      • Phenotype data
      • Point Cloud Data
    • How to Access Data
      • Using Clowder (Sensor and Genoomics data)
      • Using Globus (Sensor and Genomics data)
      • Using BETYdb (trait data, experimental metadata)
        • Accessing BETYdb via ArcMap and other GIS software
      • Using CoGe (Genomics)
      • Using CyVerse (Genomics)
      • Using Analysis Workbench (all data)
    • Data Use Policy
    • Manuscripts and Authorship Guidelines
    • Release / reprocessing schedule
  • Technical Documentation
    • Data Standards
      • Existing Data Standards
      • Agronomic and Phenotype Data Standards
      • Genomic Data Standards
      • Sensor Data Standards
      • Data Standards Committee
    • Directory Structure
    • Data Storage
    • Data Transfer
    • Data Processing Pipeline
      • Geospatial Time Series Structure
    • Data Backup
    • Data Collection
    • Data Product Creation
      • Genomic Data
      • Hyperspectral Data
    • Quality Assurance and Quality Control
    • Systems Configuration
  • Developer Manual
    • Submitting data to Clowder
    • Submitting data to BETYdb
    • Submitting Data to CoGe
    • Developing Clowder Extractors
  • Tutorials
  • Appendix
    • Code of Conduct
    • Collaboration Tools
    • Glossary
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  • Whole-genome resequencing
  • Raw data
  • Derived data
  • Genotyping-by-sequencing (GBS)
  • Raw data
  • Derived data
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  1. User Manual
  2. Data Products

Genomics data

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Last updated 6 years ago

Genomic data includes whole-genome resequencing data from the HudsonAlpha Institute for Biotechnology, Alabama for 384 samples for accessions from the sorghum (BAP) and genotyping-by-sequencing (GBS) data from Kansas State University for 768 samples from a population of sorghum recombinant inbred lines (RIL).

These data are available to Beta Users and require permission to access. The form to sign up for our beta user program is at . Once you have signed up for our beta user program you can access genomics data in one of the following locations:

  • Download via .

  • The , which provides container-based computing environments including Jupyter, Rstudio, and Python IDE.

  • The for download or use within the CyVerse computing environment.

  • The computing environment.

See before continuing.

The data is structured on both the TERRA-REF strorage (accessible via Globus and Workbench) and CyVerse Data Store infrastructures as follows:

|-terraref
|  |-genomics
|  |  |-raw_data
|  |  |  |-bap
|  |  |  |  |-resequencing
|  |  |  |-ril
|  |  |  |  |-gbs
|  |  |-derived_data
|  |  |  |-bap
|  |  |  |  |-resequencing
|  |  |  |  |  |-danforth_center
|  |  |  |-ril
|  |  |  |  |-gbs
|  |  |  |  |  |-kansas_state

Whole-genome resequencing

Raw data

Derived data

Data derived from analysis of the raw resequencing data at the Danforth Center (version1) are available as gzipped, genotyped variant call format (gVCF) files and the final combined hapmap file.

Genotyping-by-sequencing (GBS)

Raw data

Derived data

Combined genotype calls are available in VCF format.

Raw data are in bzip2 FASTQ format, one per read pair (*_R1.fastq.bz2 and *_R2.fastq.bz2). 384 samples are available. For a list of the lines sequenced, see the .

Raw data are in gzip FASTQ format. 768 samples are available. For a list of lines sequenced, see the .

Bioenergy Association Panel
http://terraref.org/beta
Globus
NDS Analysis Workbench
CyVerse Data Store
CoGe
Data use policy
sample table
sample table