Now try running the test data in Galaxy to see if you get the same results. You should probably try running from the history first and then try adding the test data as a built-in genome via the bowtie2_indexes.loc table Best, J. On Feb 15, 2013, at 12:18 AM, Sachit Adhikari wrote:

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.