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
>  
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