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


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