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Question: Need help with "Tophat for Illumina" tool
1
gravatar for elsayedhejazy
4.6 years ago by
elsayedhejazy • 10
Egypt
elsayedhejazy • 10 wrote:

Dear All,

Hello amazing Galaxy team members 

now i have 14 manipulated fastq files 7 forward and 7 reverse i need to make just one merged forward and just one merged reverse to run Tophat for paired end sequences how can i make it ?

 

Creating one file for the seven forward resulting one output file 

Creating one file for the seven reverse resulting one output file 

take tow and run tophat for paired end 

waiting your reply 

elsayedhegazy@gmail.com

 

Tool name: Tophat for Illumina
Tool version: 1.5.0
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/tophat/tophat/1.5.0
ToolShed URL: http://toolshed.g2.bx.psu.edu/view/devteam/tophat

 
tophat-for-illumina • 1.3k views
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modified 4.6 years ago by Mark Crowe • 100 • written 4.6 years ago by elsayedhejazy • 10
3
gravatar for Mark Crowe
4.6 years ago by
Mark Crowe • 100
QFAB, Brisbane
Mark Crowe • 100 wrote:

Hello elsayedhegazy

I think that the tool you're after is "Concatenate datasets tail-to-head", in the "Text Manipulation" toolbox. Just select your first fastq file in the dropdown box, and then click "Add new Dataset" and select the relevant for each of the remaining six fastqs. Repeat the process for the seven reverse files. That will give you two files ready for submission to Tophat. 

Cheers

Mark
ADD COMMENT • link written 4.6 years ago by Mark Crowe • 100
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