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Question: Cuffdiff output_version 2.2.1.1
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gravatar for franziska.denk
3.5 years ago by
franziska.denk • 0
European Union
franziska.denk • 0 wrote:

It seems that the new version of the cuffdiff tool on the main galaxy mirror outputs an sqlite database ready to input into cummeRbund. However, you don't have the cummeRbund tool implemented? 

What is the fastest way to get my output files extracted? I tried using RSQlite in R on my desktop but seem to be having some issues...

Thanks,

Franziska
cummerbund sqlite cuffdiff • 1.3k views
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modified 3.5 years ago • written 3.5 years ago by franziska.denk • 0

That's great thanks! looking forward to it. 

ADD REPLY • link written 3.5 years ago by franziska.denk • 0

done, see the edit on my answer

ADD REPLY • link written 3.5 years ago by Martin Čech ♦♦ 4.9k
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gravatar for Martin Čech
3.5 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

Shortly the cuffdiff 2.2.1.2 will be made available on usegalaxy.org taht will restore the functionality to output tabular files (so you can choose whether you want to use sqlite or tabular output). I will update this post when it is ready. Sorry for the inconvenience.

Relevant post: cuffdiff & cummerbund

 

edit: new cuffdiff is live on Main (https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.2)
ADD COMMENT • link modified 3.5 years ago • written 3.5 years ago by Martin Čech ♦♦ 4.9k
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