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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CuffDiff 

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Cuffdiff used GTF2/GFF3 annotatiuon files of transcripts, along with two or more SAM/BAM files containing the read alignments. It compares expression levels at the level of transcripts, primary transcripts, and genes.

Cuffdiff

Community rating: ?????

Cuffdiff performs differential transcript abundance analysis for two or more RNA-Seq samples.

Cuffdiff uses GTF2/GFF3 annotation files of transcripts, along with two or more SAM/BAM files containing the read alignments. It compares expression levels at the level of transcripts, primary transcripts, and genes.

Quick Start

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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3 Comments

  1. ★★★★☆ null (by vaughn)

  2. ★★★★☆ null (by vaughn)

  3. ★★★★★ It would be five start if the volcano and scatter plots worked. In addition, including a scatter plot with genes filtered to a 0.01 P value would also be useful. (by dr_richard_barker)