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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Items in PURPLE and links are the things you must modify. Change PURPLE items to BLACK when you save your page.

Cuffdiff2 with JS option (USER MANUAL UNDER DEVELOPMENT)

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Cuffdiff2 performs differential transcript abundance analysis for two or more RNA-Seq samples. However, Cuffdiff2 by default refrains from performing significance tests (Jensen-Shannon) when one of the conditions involved has fewer than three replicates for computing differential splicing, CDS switching, and promoter switching analyses. The "Cuffdiff2 with JS option" specifically addresses this by providing option to specify the number of replicates that will allow Cuffdiff2 to compute the JS tests for these analyses.

Quick Start

  • To use Cuffdiff2 with JS option
    • import your BAM files and your GTF file

Resources:http://cufflinks.cbcb.umd.edu/http://cufflinks.cbcb.umd.edu/tutorial.html and http://cufflinks.cbcb.umd.edu/howitworks.html#hdif

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 ->cuffdiff

Input File(s)

Use the following files from the directory above as test input:

 hy5_rep1.bam

  hy5_rep2.bam

  merged_with_ref_ids.gtf

  WT_rep1.bam

  WT_rep2.bam

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, and WT vs hy5 sample names

Output File(s)

Expect a 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

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