Running Tuxedo Pipeline in UGENE

The RNA-seq pipeline “Tuxedo” consists of the TopHat spliced read mapper, that internally uses  Bowtie or Bowtie 2 short read aligners, and several Cufflinks tools that allows one to assemble transcripts, estimate their abundances, and tests for differential expression and regulation in RNA-Seq samples.

...

...

Environment requirements:

• The pipeline is currently available on Linux and Mac OS X only.
• Before proceeding, please make sure Python 2.7 is installed on the target computer.

...

To run a pipeline, use UGENE Workflow Designer. To open it select Tools -> Workflow Designer in the UGENE main menu. To read more about the Workflow Designer see UGENE documentation page. To run the pipeline you may use example data from the Sample Data Package that goes with this tutorial.

...

Select Samples tab on the Workflow Designer Palette. The NGS group of samples contains two variants of the Tuxedo pipeline. Depending on the input RNA-seq short reads double-click either on Tuxedo: single-end reads or Tuxedo: paired-end reads sample.

...

Select Samples tab on the Workflow Designer Palette and double-click on the ChIP-seq analysis with Cistrome tools sample. The following configure wizard appears:

<center>
  <br>
  <img src="/wiki/download/attachments/3244623/RNA-seq analysis with Tuxedo tools_1.png"/>
  <br> 
</center>

Here you need to choose analysis type and short reads type and click Setup. There are two short reads type: single-end and paired-end reads. For both of them there are three analysis type:

1. Full Tuxedo Pipeline - use this pipeline to analyze multiple samples with TopHat, Cufflinks, Cuffmerge and Cuffdiff tools.
2. Single-sample Tuxedo Pipeline - use this pipeline to analyze a single sample with TopHat and Cufflinks tools.
3. No-new-transcripts Tuxedo Pipeline - use this pipeline to analyze multiple samples with TopHat and Cuffdiff tools only, i.e. without producing new transcripts.

For Full Tuxedo Pipeline analysis type and single-end reads type the following workflow appears:

<center>
  <br>
  <img src="/wiki/download/attachments/3244623/RNA-seq analysis with Tuxedo tools_2.png"/>
  <br> 
</center>

For Full Tuxedo Pipeline analysis type and paired-end reads type the following workflow appears:

<center>
  <br>
  <img src="/wiki/download/attachments/3244623/RNA-seq analysis with Tuxedo tools_3.png"/>
  <br> 
</center>

For Single-sample Tuxedo Pipeline analysis type and single-end reads type the following workflow appears:

<center>
  <br>
  <img src="/wiki/download/attachments/3244623/RNA-seq analysis with Tuxedo tools_4.png"/>
  <br> 
</center>

For Single-sample Tuxedo Pipeline analysis type and paired-end reads type the following workflow appears:

<center>
  <br>
  <img src="/wiki/download/attachments/3244623/RNA-seq analysis with Tuxedo tools_5.png"/>
  <br> 
</center>

For treatment tags only analysis type the following workflow appears:

Running pipeline with single-end reads 

...