Question: where can I get Info files for CummeRbund from Galaxy cuffdiff?
0
gravatar for bixdw
3.0 years ago by
bixdw0
United Kingdom
bixdw0 wrote:

Hello,

I am working with CummeRbund package for Cuffdiff output. It is a great package that makes the analysis a lot easier. However Galaxy cuffdiff output does not contain any info files which are required for replicate analysis of CummeRbund. Is there a way to retrive these files? Thank you for any help you can provide guys

Best wishes

cummerbund galaxy output cuffdiff • 1.7k views
ADD COMMENTlink modified 2.9 years ago by rossi0 • written 3.0 years ago by bixdw0
0
gravatar for Jennifer Hillman Jackson
3.0 years ago by
United States
Jennifer Hillman Jackson24k wrote:

Hello,

Is it this repository in use? https://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund

That is the most current version of the Cummerbund tool. If using Cuffdiff with the option "Include Read Group Datasets" as "Yes", these together allow replicate analysis.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.0 years ago by Jennifer Hillman Jackson24k
0
gravatar for bixdw
3.0 years ago by
bixdw0
United Kingdom
bixdw0 wrote:

Hello,

 

Thank you for the reply. I am running the cuffdiff on the main gagalxy server. I do not have access to the local Galaxy instance. Indeed when I include the Read Group Data there adittional; group_tracking files. Unfortunately CummeRbund also needs the .info files to use full range of funtions in the package. Are there plans to make these files downloadable? Or is there a way of retriveing these files by other means?

 

BW

ADD COMMENTlink written 3.0 years ago by bixdw0

Hi, I have a similar problem. I'm too using the Galaxy Main Public server usegalaxy.org) and cuffdiff outputs tried to generate a CummeRbund SQLite db (where in the previous Galaxy's release all the CummeRbund files were obtained as the Cuffdiff output). I receive an error and the SQLite db is not created and I do not see any way to obtain the original Cuffdiff output files (in order to download them and use them in R/CummeRbund locally). 

Being honest I've been experiencing quite a number of errors, slow downs and page crashes in the Usegalaxy.org instance during these last three days...

ADD REPLYlink written 2.9 years ago by rossi0
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