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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Cuffmerge 2.2.1

Community rating: ?????

Cuffmerge merges together several Cufflinks assemblies. It also handles running Cuffcompare. The main purpose of this script is to make it easier to make an assembly GTF file suitable for use with Cuffdiff.

Quick Start

Test Data

Icon

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> cuffmerge

Input File(s)

Use

 WT_rep1_transcripts.gtf

  hy5_rep1_transcripts.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.

 

  • Default parameters only, no further configuration needed.

 

Output File(s)

Expect   

merged.gtf and

merged_with_ref_ids.gtf

 as output.

Tool Source for App

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3 Comments

  1. ★★★★☆ null (by vaughn)

  2. ★★★★☆ null (by vaughn)

  3. ★★★★★ null (by dr_richard_barker)