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LEARNING MATERIALS
Maintenance: Tues, 28 Jan 2020

ACCESS TO OR USAGE OF THE FOLLOWING SERVICES WILL BE UNAVAILABLE OR DISRUPTED:

Discovery Environment         8:00am to 5:00pm MST
The Discovery Environment will be unavailable while patches and updates are applied.
        ** Currently running analyses will be terminated. Please plan accordingly.

Data Store                    8:00am to 5:00pm MST
The Data Store will be unavailable during the maintenance period.
 
Data Commons                  8:00am to 5:00pm MST
The Data Commons will be unavailable during the maintenance period.
 
Atmosphere and Cloud Services 8:00am to 5:00pm MST
Marana Cloud: Atmosphere instances in the Marana Cloud will be operational; however, you will not be able to use the Data Store within your instance, and you may not be able to access the Atmosphere web interface.
 
User Portal                   8:00am to 5:00pm MST
The User Portal, http://user.cyverse.org, will be unavailable while we perform maintenance and updates.
 
Agave/Science API             8:00am to 5:00pm MST
The Agave/Science API will be unavailable during this maintenance period.
 
DNA Subway                    8:00am to 5:00pm MST
DNA Subway will be unavailable during this maintenance period.
 
The following services will NOT be affected by the maintenance: CyVerse Wiki and JIRA 

Keep up to date with our maintenance schedules on the CyVerse public calendar
http://www.cyverse.org/maintenance-calendar
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  1. A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)

  2. Input/Outputs 
    1. Transcript file(s) in FASTA format (Mandatory)
    2. Output directory to store all results.
  3. Options/Parameters
    1.  Run with GeneMarkS-T gene prediction tool. Use `--prokaryote` option if the genome is prokaryotic. Eukaryote is default.
    2. Run BUSCO tool, which detects core genes in the assembly. BUSCO lineage data (Eukaryota, Metazoa, Arthropoda, Vertebrata or Fungi). You can select the BUSCO profile files for your species of interest from here : /iplant/home/shared/iplantcollaborative/example_data/BUSCO.sample.data
    3. Run disable_infer_genes option if your GTF file already contains genes records, otherwise gffutils will fix it. Note that gffutils may work for quite a long time.
    4. Run disable_infer_transcripts if your GTF file already contains transcripts records, otherwise gffutils will fix it. Note that gffutils may work for quite a long time.
    5. Name(s) of assemblies that will be used in the reports separated by space and given in the same order as files with transcripts / alignments.
    6.  Set if transcripts were assembled using strand-specific RNA-Seq data in order to benefit from knowing whether the transcript originated from the + or - strand.
    7.  Do not draw plots (makes rnaQUAST run a bit faster).

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