The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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HTProcess_CuffDiff-2.2.0

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Quick Start

  • To use HTProcess_CuffDiff-2.2.0, 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_Cuffmerge from multiple HTProcess_Cufflinks assemblies.
  • Resources: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/

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 -> HTProcess_CuffDiff ->inputs

Input File(s)

Use 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.

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

Output File(s)

Expect 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

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