hg19 reference gnome for Tophat2
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 genome.rev.1.bt2 genome.rev.2.bt2 While adding the reference gnome, I need to edit bowtie2_indices.loc Shall I replace: /orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 with hg19 hg19 hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index Thanks, Sachit
Also, do I have make all the reference files executable? On Wed, Feb 13, 2013 at 6:39 AM, Sachit Adhikari < sachit.technerves@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. 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 genome.rev.1.bt2 genome.rev.2.bt2
While adding the reference gnome, I need to edit bowtie2_indices.loc
Shall I replace:
/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19
with
hg19 hg19 hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index
Thanks,
Sachit
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.
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.
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.
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.
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.
participants (2)
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Jeremy Goecks -
Sachit Adhikari