Jonas,

Cuffmerge and Cuffcompare use the sam_fa_indices.loc for sequence data; this is done for historical reasons.

You can see this if you take a look at the wrapper code: <galaxy_home>/tools/ngs_rna/cuffmerge_wrapper.py <galaxy_home>/tools/ngs_rna/cuffcompare_wrapper.py

Best,
J.

On Oct 19, 2012, at 6:10 AM, Jonas Grauholm wrote:

Greetings,
 
I’m trying to analyse a number of mouse RNA-seq samples on a local galaxy install. When trying to run cuffmerge and cuffcompare I get the following error.
 
No sequence data found for dbkey M_musculus_Ensembl_NCBIM37, so sequence data cannot be used.
 
The tool works fine with a human reference genome so im fairly confident I just fumbled a config file somewhere.
The problem is I been having difficulty locating exactly what file defines what sequence file is being used?
 
I looked through all my config files but so far I been unable to locate the error, could anyone possibly point me in the right direction?
 
Best Regards
 
Jonas Grauholm
AROS Applied Biotechnology A/S
SciencePark Skejby
Brendstrupgaardsvej 102
DK+8200 Aarhus N
Phone: +45 70271170
 
___________________________________________________________
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/