Versions Compared


  • This line was added.
  • This line was removed.
  • Formatting was changed.


Community rating: ?????

TopHat 2.0.11 is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the short read aligner Bowtie and analyzes the mapping results to identify splice junctions between exons.

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 -> htprocess > HTProcess_trimmomatic.

Input File(s)

Use the HTProcess_Reads_T1 directory from the HTProcess_trimmomatic directory within the directory above as test input, and the reference fasta file in the sample_input_files directory in the directory above.

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_BAM_condition as output, where condition is defined originally in the HTProcess_prepare_directories_and_run_fastqc by the condition setting. For the test case, the output directory you will find in the example_data directory is named HTProcess_BAM_control.

Tool Source for App




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