Question: cummeRbund missing files
1
gravatar for ajmaninisha
3.2 years ago by
ajmaninisha30
Canada
ajmaninisha30 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

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by ajmaninisha30
1
gravatar for Dannon Baker
3.2 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k 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 COMMENTlink written 3.2 years ago by Dannon Baker3.7k

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 REPLYlink written 3.2 years ago by ajmaninisha30
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 REPLYlink written 3.2 years ago by Dannon Baker270
0
gravatar for ajmaninisha
3.2 years ago by
ajmaninisha30
Canada
ajmaninisha30 wrote:

Should i re run it again

ADD COMMENTlink written 3.2 years ago by ajmaninisha30
1

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

ADD REPLYlink written 3.2 years ago by Dannon Baker3.7k
0
gravatar for ajmaninisha
3.2 years ago by
ajmaninisha30
Canada
ajmaninisha30 wrote:

Hi,

Is the server updated?

 

Thanks

 

 

 

Regards

Nisha

ADD COMMENTlink written 3.2 years ago by ajmaninisha30
0
gravatar for ajmaninisha
3.2 years ago by
ajmaninisha30
Canada
ajmaninisha30 wrote:

Kindly advise

ADD COMMENTlink written 3.2 years ago by ajmaninisha30
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