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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HTProcess_Cuffmerge-1

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Run cuffmerge on all gtf files in input directories.

Quick Start

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 -> htprocess1

Input File(s)

Use the directory named HTProcess_Cufflinks_control and the directory named HTProcess_Cufflinks_dehydrated from the HTProcess_Cufflinks directory, which is in the directory listed 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.

  • Default parameters only, no further configuration needed.

Output File(s)

Expect a directory named HTProcess_Cuffmerge, and a file named merged_with_ref_ids.gtf as output. For the test case, the output directory and file are in the HTProcess_cuffmerge directory in the directory listed above for test data.

Tool Source for App

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