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:
    1. Genome name: Name of the genome
    2. kmer: Size of the kmer that you want to use
    3. Genome fasta file (mandatory): Path to the genome fasta file
    4. gmapdb directory: Destination directory name

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

Input File(s)

Inputs:

    1. Genome name: test_genome
    2. kmer: 15
    3. Genome fasta file (mandatory): genome.fa
    4. gmapdb directory: gmapdb

Output reports:

Expect a folder named gmapdb which you can use with gmap-2018.03.25 for mapping the reads against

Tool Source for App

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