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

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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

Info

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

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