Hi Jeremy,

I was successfully able to run the test data from the tophat2 website in command line. I think there's something wrong with the reference genome. I have correctly specified the path of reference genome? What's the problem I am facing?

On Thu, Feb 14, 2013 at 1:44 PM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:

Try using the Tophat test data to verify your installation; it's known to have splice junctions:

http://tophat.cbcb.umd.edu/tutorial.html

http://tophat.cbcb.umd.edu/downloads/test_data.tar.gz

Good luck,

J.

On Feb 14, 2013, at 6:29 AM, Sachit Adhikari wrote:

I tried with many data but still the same problem and regarding settings I haven't changed a thing of Tophat2. What might be causing this error? 

Thanks

On Wed, Feb 13, 2013 at 7:10 PM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:

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.goecks@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.