missing 'Alignment Gap/Insertion Display Options' section for custom BAM track
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David Hoover
Oct 30, 2014, 3:42:58 PM10/30/14
to genome...@soe.ucsc.edu
Hi,
When I create a custom track on the UCSC site, the track settings shows a section titled 'Alignment Gap/Insertion Display Options'. However, if I create the same custom track on our local mirror, this section is missing.
Both the UCSC and the local mirror are v307.
Is there something missing or disabled? What controls the sections shown in track displays?
Wondering,
David
--------------------
David Hoover, PhD
Helix Systems Staff
SCB/DCSS/CIT/NIH
301-435-2986
http://helix.nih.gov
When I create a custom track on the UCSC site, the track settings shows a section titled 'Alignment Gap/Insertion Display Options'. However, if I create the same custom track on our local mirror, this section is missing.
Both the UCSC and the local mirror are v307.
Is there something missing or disabled? What controls the sections shown in track displays?
Wondering,
David
--------------------
David Hoover, PhD
Helix Systems Staff
SCB/DCSS/CIT/NIH
301-435-2986
http://helix.nih.gov
David Hoover
Oct 30, 2014, 5:08:19 PM10/30/14
to David Hoover, genome...@soe.ucsc.edu
Never mind. Another hidden option in hg.conf that I had not found yet.
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Matthew Speir
Oct 30, 2014, 7:27:19 PM10/30/14
to David Hoover, David Hoover, genome...@soe.ucsc.edu
Hi David,
Thank you for your question about the "Alignment Gap/Insertion Display Options" for custom BAM tracks. I'm glad that you were able to find the trackDb settings that you needed to make these options available for your custom BAM track. Would you be willing to share these settings with the rest of the list? This may help other users who run into a similar issue. We will also look into adding new documentation for these trackDb settings on our Track Database Definition document, under the BAM section: http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#bam.
I hope this is helpful. If you have any further questions, please reply to genome...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
Thank you for your question about the "Alignment Gap/Insertion Display Options" for custom BAM tracks. I'm glad that you were able to find the trackDb settings that you needed to make these options available for your custom BAM track. Would you be willing to share these settings with the rest of the list? This may help other users who run into a similar issue. We will also look into adding new documentation for these trackDb settings on our Track Database Definition document, under the BAM section: http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#bam.
I hope this is helpful. If you have any further questions, please reply to genome...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
--
David Hoover
Oct 31, 2014, 12:11:59 PM10/31/14
to Matthew Speir, genome...@soe.ucsc.edu
It was not so much hidden, as it was unknown to me. In the example hg.conf that comes with the mirror download,
kent/src/product/ex.hg.conf
there is this little nugget:
# New browser function as of March 2007. Future browser code will
# have this on by default, and can be turned off with =off
# Initial release of this function requires it to be turned on here.
browser.indelOptions=on
David
--------------------
David Hoover, PhD
Helix Systems Staff
SCB/DCSS/CIT/NIH
301-435-2986
http://helix.nih.gov
kent/src/product/ex.hg.conf
there is this little nugget:
# New browser function as of March 2007. Future browser code will
# have this on by default, and can be turned off with =off
# Initial release of this function requires it to be turned on here.
browser.indelOptions=on
David
--------------------
David Hoover, PhD
Helix Systems Staff
SCB/DCSS/CIT/NIH
301-435-2986
http://helix.nih.gov
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