This app has been deprecated and is no longer available. Please use a Hisat2 app in the DE, which more efficiently and accurately provides the same core functionality (i.e., spliced alignment of RNA-Seq reads). If you cannot find a suitable replacement, please contact CyVerse Support at email@example.com.
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Items in PURPLE and links are the things you must modify. Change PURPLE items to BLACK when you save your page.
TopHat Aligner for Paired-End Illumina Reads (Custom Genome)
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Use TerriblyIncomprehensible.txt and HorriblyWritten.txt 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.
Use either the "Default parameters..." section OR fill in the "Use these parameters..." section. Delete the unused section and the OR. Then, delete this note.
Expect a text file named after the input files as output. For the test case, the output file you will find in the example_data directory is named BeautifulProse.txt.
Tool Source for App