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 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.eduwrote:
If the other outputs are fine, then the problem is likely with
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
Shall I replace:
/orig/path/hg19hg19hg19
/depot/data2/galaxy/bowtie2/hg19/hg19
with
hg19 hg19hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index
Yes, that's correct.
Finally, please email only galaxy-dev with questions about local installations;
Also, do I have make all the reference files executable?
No, that's not necessary.
Best,
J.
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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.eduwrote:
Shall I replace:
/orig/path/hg19hg19hg19
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?
I downloaded the entire directory of UCSC for the reference gnome of
Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference
gnome. I found a directory: Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index
with the files:
genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2
Also, do I have make all the reference files executable?
On Wed, Feb 13, 2013 at 6:39 AM, Sachit Adhikari
sachit.techner...@gmail.com wrote:
I downloaded the entire directory of UCSC for the reference gnome of
Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference
gnome.
