Hi,

Cuffdiff in Galaxy produces "read_group_tracking" files. However, I wonder if 
these files are enough when using 'replicates=T' in cummeRbund or I also need 
"read_groups.info" and "run.info" files in myDir.

I've tried 'replicates(cuff)' with the 'read_group_tracking' files in my 
directory and I get back an empty set, means that cummerbund is not using 
replicates (or I'm doing something wrong!). At this time I don't see other 
option that run cuffdiff locally. At least you have any suggestion or advice 
about how I can get 'info.files' from Galaxy.

Any particular reason why Cuffdiff output files in Galaxy are not ALL the files 
described in the manual tool?

Thanks for you help.



Elihu

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

Reply via email to