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Question: cummeRbund missing files
1
gravatar for ajmaninisha
3.7 years ago by
ajmaninisha • 30
Canada
ajmaninisha • 30 wrote:

Hi,

i want to run cummeRbund in R from my cuffdiff output files but galaxy doesnot gives me count files and some of the files are with the same name , kindly advise how can i use them in R it doesnot accepts the file given by galaxys and sometimes gives error and sometimes:

 

Genes 0

isoforms 0

cds 0

tss 0

 

Kindly advise
in r all files cummerbund files • 1.0k views
ADD COMMENT • link •
modified 3.6 years ago • written 3.7 years ago by ajmaninisha • 30
1
gravatar for Dannon Baker
3.7 years ago by
Dannon Baker ♦ 3.7k
United States
Dannon Baker ♦ 3.7k wrote:

I'm almost positive this is a bug we've just tracked down and fixed within the last 24 hours.  Are you trying to run this on usegalaxy.org?  If so, the change hasn't made it there yet, but will soon.
ADD COMMENT • link written 3.7 years ago by Dannon Baker ♦ 3.7k

Hi,

I am running this on usegalaxy.org. This has happened twice. Also, i want to run cummeRbund in R by using cuffdiff output files from galaxy. But R platform, does not recognizes these files and they have different file names in the manual. Kindly advise how can i use them , are they not compatible in the R platform.

ADD REPLY • link written 3.7 years ago by ajmaninisha • 30
1

We're working on getting the update to the main Galaxy server and this should resolve your issue.  I can update this question when that happens.

ADD REPLY • link written 3.7 years ago by Dannon Baker • 270
0
gravatar for ajmaninisha
3.7 years ago by
ajmaninisha • 30
Canada
ajmaninisha • 30 wrote:

Should i re run it again
ADD COMMENT • link written 3.7 years ago by ajmaninisha • 30
1

Not until we've updated the server -- there won't be any difference.

ADD REPLY • link written 3.7 years ago by Dannon Baker ♦ 3.7k
0
gravatar for ajmaninisha
3.7 years ago by
ajmaninisha • 30
Canada
ajmaninisha • 30 wrote:

Hi,

Is the server updated?

 

Thanks

 

 

 

Regards

Nisha
ADD COMMENT • link written 3.7 years ago by ajmaninisha • 30
0
gravatar for ajmaninisha
3.6 years ago by
ajmaninisha • 30
Canada
ajmaninisha • 30 wrote:

Kindly advise
ADD COMMENT • link written 3.6 years ago by ajmaninisha • 30
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