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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Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

Quick Start

Test Data


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

Input File(s)

Use the fastq files, SRR567164sra_1.fastq and SRR567164sra_2.fastq from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

The sequence format is set to fastq and the strand-specific library type is set to FR. Otherwise the parameters used are default.

Output File(s)

Expect a fasta file as output. For the test case, the output file you will find in the example_data directory is named Trinity.fasta. There is also a large collection of intermediate files.

Tool Source for App

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