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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Tuxedo pipeline

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(up to four conditions)

This workflow carries out differential expression analysis using the Tuxedo suite of tools. In this workflow: TopHat v2.0.9, Cufflinks package (including Cuffmerge and Cuffdiff) v2.2.1 and CummeRbund 2.4.1-1.

Quick Start

Test Data

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Test data for this app are temporarily not available in the Discovery Environment.

Input File(s)

Input files required: 

  1. Paired end sequencing RNA-seq reads for each condition/replicate
  2. A reference genome in Fasta format OR select reference genome hosted on iPlant from drop down menu
  3. A genome annotation file in GFF3 or GTF2 format (http://cole-trapnell-lab.github.io/cufflinks/file_formats/) OR select annotation hosted on iPlant from drop down menu
  4. OPTIONAL- GTF masking file (containing transcripts to be ignored)

Parameters Used in App

The tool settings in the app can be changed but are set as the default values (as dictated by each program in the workflow). If you are using the Tuxedo suite of tools for the first time we recommend using the default values in the first instance.

Tool Source for App

Program manuals:

  1. Tophat https://ccb.jhu.edu/software/tophat/manual.shtml
  2. Cufflinks-Cuffdiff http://cole-trapnell-lab.github.io/cufflinks/manual/
  3. CummeRbund http://compbio.mit.edu/cummeRbund/manual_2_0.html
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