HTProcess_Tophat 2.0.13
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Quick Start
- To use HTProcess_Tophat-2.0.13, your data must be in the form of the output directory for HTProcess_trimmomatic, HTProcess_Reads_T1
- Resources: https://pods.iplantcollaborative.org/wiki/display/~rogerab/A+rough+entry+on+how+to+use+the+HTProcess+apps.
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 as test input the HTProcess_Reads_T1 directory from the HTProcess_trimmomatic.subdirectory in the directory above.
Use BASoapOutput47.scafSeq_gapcloser.fa in the sample_input_files > references directory.
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 BAM files named after the input files output in the HTProcess_BAM_condition directory. For the test case, the output directory you will find in the example_data directory is named HTProcess_BAM_control.
Tool Source for App
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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 support@cyverse.org. |