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  • To use Cuffdiff2 with JS option, 
    • import your
    data in ___ format.
    • BAM files and your GTF file




... and

Test Data



Test data for this app appears directly in the Discovery Environment in the Data window


under Community Data -> iplantcollaborative -> example_data ->



Input File(s)

Use TerriblyIncomprehensible.txt and HorriblyWritten.txt Use the following files 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


  • Default parameters only, no further configuration needed.


  • Use these parameters within the DE app interface:
    • parameter name - value/setting
    • parameter name - value/setting
  • only, and WT vs hy5 sample names

Output File(s)

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.series of files describing the expression for genes and transcripts as output in a cuffdiff_out directory and a series of sorted files of significantly features that have significantly different expression in the sorted_data directory. 

Tool Source for App