HTProcess_Cufflinks-2.2.0
HTProcess_Cufflinks-2.2.0
An app for use with the output from the HTProcess Tophat app.
Quick Start
- To use HTProcess_Cufflinks-2.2.0, import your data in HTProcess pipeline format, specifically the HTProcess_BAM_condition directory output by HTProcess_Tophat-2.0.11.
- *Resources: https://github.com/cole-trapnell-lab/cufflinks
Test Data
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 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.
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_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.
Tool Source for App
- *Resources: https://github.com/cole-trapnell-lab/cufflinks