Displaying genomic sequences in Trackster
Dear all, We have our own galaxy instance and the idea is to have trackster enabled for users to be able to visualize NGS mapping. We were able to configure trackster in our instance and the visualization works fine. We have two questions regarding trackster: 1) We can't display genomic sequences in trackster. As per the tutorial, we set the location of the .2bit file in the twobit.loc file for the trackster to be able to display the genomic sequence but for some reason it doesn't display it. The name of the builds is the same in all places i.e) in ucsc/chrom/builds.txt and also in the .loc files. Any ideas on what else should be done? 2) While saving the visualization, there is always an error message saying "could not save visualization" and it doesn't seem to be a web browser issue. How do we then save the visualization? Thanks in advance, Naharajan
Hi Naharajan, My best guess is that you've found some bugs. Fortunately, they are likely fixed in galaxy-central and will soon be available in galaxy-dist (we're planning an update in the next couple days). Once galaxy-dist is updated, please try updating your Galaxy instance and seeing if that fixes the problems. If not, let us know and we can take a closer look. J. On Apr 18, 2012, at 9:05 AM, Naharajan Lakshmanaperumal wrote:
Dear all,
We have our own galaxy instance and the idea is to have trackster enabled for users to be able to visualize NGS mapping. We were able to configure trackster in our instance and the visualization works fine.
We have two questions regarding trackster: 1) We can't display genomic sequences in trackster. As per the tutorial, we set the location of the .2bit file in the twobit.loc file for the trackster to be able to display the genomic sequence but for some reason it doesn't display it. The name of the builds is the same in all places i.e) in ucsc/chrom/builds.txt and also in the .loc files. Any ideas on what else should be done?
2) While saving the visualization, there is always an error message saying "could not save visualization" and it doesn't seem to be a web browser issue. How do we then save the visualization?
Thanks in advance, Naharajan
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Hi Jeremy, So, we updated our galaxy instance and now the genomic sequences can be displayed, when sufficiently zoomed in and also the visualization can be saved now. It looks really nice :-) Thanks a lot for your help. Regards, Naharajan On Apr 18, 2012, at 6:10 PM, Jeremy Goecks wrote:
Hi Naharajan,
My best guess is that you've found some bugs. Fortunately, they are likely fixed in galaxy-central and will soon be available in galaxy-dist (we're planning an update in the next couple days). Once galaxy-dist is updated, please try updating your Galaxy instance and seeing if that fixes the problems.
If not, let us know and we can take a closer look.
J.
On Apr 18, 2012, at 9:05 AM, Naharajan Lakshmanaperumal wrote:
Dear all,
We have our own galaxy instance and the idea is to have trackster enabled for users to be able to visualize NGS mapping. We were able to configure trackster in our instance and the visualization works fine.
We have two questions regarding trackster: 1) We can't display genomic sequences in trackster. As per the tutorial, we set the location of the .2bit file in the twobit.loc file for the trackster to be able to display the genomic sequence but for some reason it doesn't display it. The name of the builds is the same in all places i.e) in ucsc/chrom/builds.txt and also in the .loc files. Any ideas on what else should be done?
2) While saving the visualization, there is always an error message saying "could not save visualization" and it doesn't seem to be a web browser issue. How do we then save the visualization?
Thanks in advance, Naharajan
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
On Apr 18, 2012, at 9:05 AM,
Naharajan Lakshmanaperumal wrote:
Dear all, We have our own galaxy instance and the idea is to have
We have two questions regarding trackster: 1) We can't display genomic sequences in trackster. As per the tutorial, we set the location of
trackster enabled for users to be able to visualize NGS mapping. We were able to configure trackster in our instance and the visualization works fine. the .2bit
file in the twobit.loc file for the trackster to be able to display the genomic sequence but for some reason it doesn't display it.
Hello! I am trying to enable Trackster on our local galaxy to visualize the mapping results. But, so far, it is not working. Is the twobit.loc file necessary for using Trackster? or is it just optional? Best regards, Menorca
Hello! I am trying to enable Trackster on our local galaxy to visualize the mapping results. But, so far, it is not working. Is the twobit.loc file necessary for using Trackster? or is it just optional?
Best regards, Menorca
Twobit files, configured via twobit.loc, are optional. Here is a page that lists all the steps required to get Galaxy genome visualizations (including Trackster) working: http://wiki.galaxyproject.org/Visualization%20Setup Let us know if you run into any problems or have questions. Thanks, J.
participants (3)
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Jeremy Goecks -
menorca -
Naharajan Lakshmanaperumal