Cuffmerge2

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Cuffmerge2 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.

Cuffmerge2 provides an interface to Cuffmerge 2+ to merge reference GTF files for multple Cufflinks outputs. This step is recommended by the authors of the Cufflinks package.

App Creator

Sheldon Mckay

Quick Start

• To use Cuffmerge2, import 2 or more gtf files produced by Cufflinks
• Resources: http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/
   

Test Data

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.

Related Tutuorials

RNA-Seq Tutorial (DE 1.8)

Tool Source for App

http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/