If the other outputs are fine, then the problem is likely with your data and/or 
your Tophat settings.

Good luck,
J.

On Feb 13, 2013, at 8:22 AM, Sachit Adhikari wrote:

> Ok sorry. I did that, but the output of splice junctions is empty. The other 
> outputs looks fine. What might be the problem?
> 
> Thanks,
> 
> Sachit
> 
> On Wed, Feb 13, 2013 at 1:20 PM, Jeremy Goecks <jeremy.goe...@emory.edu> 
> wrote:
> > Shall I replace:
> >
> > /orig/path/hg19        hg19    hg19                    
> > /depot/data2/galaxy/bowtie2/hg19/hg19
> >
> > with
> >
> > hg19   hg19    hg19   Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index
> 
> Yes, that's correct.
> 
> Finally, please email only galaxy-dev with questions about local 
> installations; galaxy-user is for questions about how to use Galaxy.
> 
> Best,
> J.
> 
> 

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