To perform bias correction using sequence data in 
Cufflinks/Cuffcompare/Cuffdiff, you'll need to set up and add entries to 
sam_fa_indices.loc 

Of course, this isn't the most intuitive place, and we're planning to improve 
loc file structure and usage in the future.

Best,
J.

On Mar 1, 2013, at 7:53 PM, Joshua Udall wrote:

> I have a local install of Galaxy. Tophat2 and Cufflinks work.  cuffcompare 
> and cuffmerge do not. Errors are below.
> 
> There isn't a .loc file for cufflinks (overall).  It will run if I don't 'use 
> sequence'.  It appears that the name of the database (dbkey) is inherited 
> from the Tophat2 output file, but it coming up empty for cuff compare and 
> cuffmerge.  
> 
> Any thoughts how I can get this to work?
> 
> 
> 
> 
> 
> 
>   
> 
> 
> 
> An error occurred running this job: cuffcompare v2.0.2 (3524M)
> No sequence data found for dbkey ?, so sequence data cannot be used.
> cp: 
> /Users/galaxy/galaxy-dist/database/job_working_directory/001/1549/cc_output.input1.tmap:
>  No such file or directory
> cp: /Users/galaxy/galaxy-dist/database/j
> 
> 
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> 
>  http://lists.bx.psu.edu/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

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

Reply via email to