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_Cufflinks-2.2.1

An app for use with the output from the HTProcess Tophat app.

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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

Use the HTProcess_BAM_control directory in the HTProcess_Tophat2 directory, which is in the directory above, as test input. The reference GFF file can be found in the sample_input_files directory under references.

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_Cufflinks_condition as output, where condition is the condition setting originally set for this library of HTProcess files. For the test case, the output file you will find in the example_data directory is named HTProcess_Cufflinks_control, and an example is provide in the HTProcess_Cufflinks directory of the main directory listed above.

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