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HTProcess_CuffDiff-2.2.0

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Quick Start

• To use HTProcess_CuffDiff-2.2.0, import your data must be completely analysed within an HTProcess pipeline, starting with HTProcess-prepare_directories_and_run_fastqc. The data to use come in the form of HTProcess_BAM directories for different read groups/conditions, and the merged .gtf annotation file for the transcriptome, created by HTProcess__ formatCuffmerge from multiple HTProcess_Cufflinks assemblies.
• Resources: http://replace.with.URL.for.tool.documentation.from.the.tool.source.orgcole-trapnell-lab.github.io/cufflinks/cuffdiff/

Test Data

Input File(s)

Use TerriblyIncomprehensible.txt and HorriblyWritten.txt from these HTProcess_BAM directories: HTProcess_BAM_cytoplasm and HTProcess_BAM_nucleus. For the annotation file, use merged_with_ref_is.gtf from the directory above as test input.

...

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.

• Default parameters only, no further configuration needed.

OR

• Use these parameters within the DE app interface:
  • parameter name - value/setting
  • parameter name - value/setting

the default settings, and the single-ended read files should be analysed independently (a separate replicate for a separate file).

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.for the test files to get the outputs provided in the Data Store at this location: Community Data -> iplantcollaborative -> example_data -> htprocess1 -> HTProcess_CuffDiff ->outputs. 

Tool Source for App

• http://replace.with.URL.for.tool.orgcole-trapnell-lab.github.io/cufflinks/cuffdiff/