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.goe...@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.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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