The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.

Please work through the tutorial and add your comments to the bottom of this page. Or send comments per email to support@cyverse.org. Thank you.

Rationale and background: 

 

GMAP is a tool for rapidly and accurately mapping and aligning cDNA sequences to genomic sequences.

  1. Inputs (mandatory):
    1. Genome directory: Path to the directory that was built using gmap_build-2018-03-25
    2. Genome database: Name of the genome database (This should match the genome name of the Genome name in the gmap_build-2018-03-25 app)
    3. Transcript fasta file: Path to the transcript fasta file
  2. Parameters:
    1. Maximum number of paths to show (default: 0)
  3. Output:
    1. Output format: Available options samse, sampe, bedpe (default is samse)

    2. Output File Name: Name of the output file (default is output.sam)

Test Data

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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> gmap > test_inputs

  1. Inputs (mandatory):
    1. Genome directory: test_genome
    2. Genome database: test_genome
    3. Transcript fasta file: test_transcripts.fa
    Parameters:
    1. Maximum number of paths to show: 0
    Output:
    1. Output format: samse

    2. Output File Name: output.sam

Output reports:

Expect a file named output.sam in your analysis output folder

Tool Source for App

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