trackster: missing graphs for large number of contigs
Hey guys, we want to use trackster in our local galaxy instance (rev. 10392:1ae95b3aa98d release_2013.08.12) and followed the instructions at http://wiki.g2.bx.psu.edu/Learn/Visualization . We tested it with a custom Build of 96 sequences in a fasta file, where all bams were mapped against before, everything worked fine. But now we want to do the same for a much larger file (about 29.000 contigs) and no graph is displayed at all, no matter which contig is used. No error appears, only the graphs are missing. Any ideas what this could be? We would be grateful for any advice. Thanks Thomas --- Thomas Berner Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants - Erwin Baur-Straße 27 06484 Quedlinburg - Germany - Phone: ++49 ( 0 ) 3946 47 562 EMail: thomas.berner@jki.bund.de
A couple questions: (a) are you using a custom build? If so, does the build show the correct number of chromosomes? (b) do you see any errors in the JavaScript console when trying to view the BAM file? Thanks, J. On Oct 21, 2013, at 11:05 AM, "Berner, Thomas" <thomas.berner@jki.bund.de> wrote:
Hey guys,
we want to use trackster in our local galaxy instance (rev. 10392:1ae95b3aa98d release_2013.08.12) and followed the instructions at http://wiki.g2.bx.psu.edu/Learn/Visualization .
We tested it with a custom Build of 96 sequences in a fasta file, where all bams were mapped against before, everything worked fine. But now we want to do the same for a much larger file (about 29.000 contigs) and no graph is displayed at all, no matter which contig is used.
No error appears, only the graphs are missing.
Any ideas what this could be? We would be grateful for any advice.
Thanks
Thomas ---
Thomas Berner
Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants - Erwin Baur-Straße 27 06484 Quedlinburg - Germany -
Phone: ++49 ( 0 ) 3946 47 562 EMail: thomas.berner@jki.bund.de
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Hi Jeremy, a) Yes, were are using a custom build and the build shows the correct number of contigs (28.592). b) There are no errors in the console. Thanks, Thomas Von: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Gesendet: Dienstag, 22. Oktober 2013 15:55 An: Berner, Thomas Cc: galaxy-dev@lists.bx.psu.edu Betreff: Re: [galaxy-dev] trackster: missing graphs for large number of contigs A couple questions: (a) are you using a custom build? If so, does the build show the correct number of chromosomes? (b) do you see any errors in the JavaScript console when trying to view the BAM file? Thanks, J. On Oct 21, 2013, at 11:05 AM, "Berner, Thomas" <thomas.berner@jki.bund.de<mailto:thomas.berner@jki.bund.de>> wrote: Hey guys, we want to use trackster in our local galaxy instance (rev. 10392:1ae95b3aa98d release_2013.08.12) and followed the instructions at http://wiki.g2.bx.psu.edu/Learn/Visualization . We tested it with a custom Build of 96 sequences in a fasta file, where all bams were mapped against before, everything worked fine. But now we want to do the same for a much larger file (about 29.000 contigs) and no graph is displayed at all, no matter which contig is used. No error appears, only the graphs are missing. Any ideas what this could be? We would be grateful for any advice. Thanks Thomas --- Thomas Berner Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants - Erwin Baur-Straße 27 06484 Quedlinburg - Germany - Phone: ++49 ( 0 ) 3946 47 562 EMail: thomas.berner@jki.bund.de<mailto:thomas.berner@jki.bund.de> ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
The good news is that it sounds like the build has been set up correctly; the bad news is that a lack of console errors gives us nothing else to go on. Would you be interested in sharing your datasets with me and I can take a look? Also, our next release is coming next week, and there are some bug fixes for Trackster that may solve your problems. Thanks, J. On Oct 28, 2013, at 4:46 AM, "Berner, Thomas" <thomas.berner@jki.bund.de> wrote:
Hi Jeremy,
a) Yes, were are using a custom build and the build shows the correct number of contigs (28.592). b) There are no errors in the console.
Thanks, Thomas
Von: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Gesendet: Dienstag, 22. Oktober 2013 15:55 An: Berner, Thomas Cc: galaxy-dev@lists.bx.psu.edu Betreff: Re: [galaxy-dev] trackster: missing graphs for large number of contigs
A couple questions:
(a) are you using a custom build? If so, does the build show the correct number of chromosomes? (b) do you see any errors in the JavaScript console when trying to view the BAM file?
Thanks, J.
On Oct 21, 2013, at 11:05 AM, "Berner, Thomas" <thomas.berner@jki.bund.de> wrote:
Hey guys,
we want to use trackster in our local galaxy instance (rev. 10392:1ae95b3aa98d release_2013.08.12) and followed the instructions at http://wiki.g2.bx.psu.edu/Learn/Visualization .
We tested it with a custom Build of 96 sequences in a fasta file, where all bams were mapped against before, everything worked fine. But now we want to do the same for a much larger file (about 29.000 contigs) and no graph is displayed at all, no matter which contig is used.
No error appears, only the graphs are missing.
Any ideas what this could be? We would be grateful for any advice.
Thanks
Thomas ---
Thomas Berner
Julius Kühn-Institut (JKI) - Federal Research Centre for Cultivated Plants - Erwin Baur-Straße 27 06484 Quedlinburg - Germany -
Phone: ++49 ( 0 ) 3946 47 562 EMail: thomas.berner@jki.bund.de
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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Berner, Thomas -
Jeremy Goecks